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Visualizing nanotechnology data with Seed Media Group and GE (General Electric)

Monday, February 11th, 2013

University of Washington (UW) researchers have uploaded a number of nanotechnology infographics on the visualizing.org website, from the UW Division of Design 2010: Nanotechnology Infographics webpage,

There are more than 1/2 dozen of these nanotechnology-themed infographics available on the page. This particular infographic, Nanotechnology:  Size Really is Everything,  has the following credit line,

By Kim Shedrick. Faculty: Karen Cheng, Marco Rolandi. Part of a series of infographics explaining nanotechnology through scale, how it has integrated into society, and what products it is being used in today.

Cheng and Rolandi have been mentioned here before in a Feb. 22, 2012 posting about their University of Washington Design Help Desk and their effort to match up scientists with designers in the interest of producing better science graphics.

I have nothing against better science graphics but I would like to know what information/data is supporting this and their other visualizations. I did resize the graphic to look more closely at the text but there were no references or citations.

Btw, The website handles ‘zooming’ in to see details clumsily. Rather than a click on the zooming tool resulting in a larger image, you are presented with an infographic which is now held within an Adobe PDF reader before you can magnify the image.

For those generally interested in infographics and visualizing date, there’s a lot to choose from on the Visualizing.org website. For those who like to dig a bit deeper, this site is a public relations ploy by General Electric and Seed Media Group. From the About Visualizing.org webpage,

Visualizing.org was created by GE and Seed Media Group to help make data visualization more accessible to the general public; to promote information literacy through the creation, sharing, and discussion of data visualizations; and to provide a unique resource to help simplify complex issues through design.

Seed Media seems to be an outgrowth (pun intended) of SEED Magazine. The magazine, which was founded by Adam Bly when he lived in Montréal, Canada, has always been focused on science and culture.  Headquarters for the magazine were moved to New York and, either at the same time or later, the magazine became a strictly online publication. From the Wikipedia essay (Note: Links have been removed),

Seed (subtitled Science Is Culture; originally Beneath the Surface) is an online science magazine published by Seed Media Group. The magazine looks at big ideas in science, important issues at the intersection of science and society, and the people driving global science culture. Seed was founded in Montreal by Adam Bly and the magazine is now headquartered in New York with bureaus around the world. May/June 2009 (Issue No. 22) was the last print issue. Content continues to be published on the website.

(I first mentioned SEED magazine in a Sept. 18, 2009 posting.) Interestingly, Seed Media which publishes the magazine makes no mention of it (that I could find) on its website. From Seed Media Group’s Learn webpage,

Scientific ThinkingTM

It’s a different way of looking at the world. It’s about using data to uncover patterns and design to confront complexity. It’s about connecting things to reveal systems. It’s about traversing scales and disregarding disciplines, applying neuroscience to economics, math to global health, virology to manufacturing, and genetics to law… It’s about experimenting all the way to understanding. It’s about changing your mind with new evidence – and getting as close to truth as humanly possible.

Getting 7 billion people to think scientifically has never been a small mission. And it has never been more important.

Since 2005, we have offered ideas and stories to help people think scientifically. Now we’re taking the next big step in this journey by creating tools and services to help institutions – companies, governments, and international organizations – do the same. We’re taking our way of seeing and thinking to parliaments, courtrooms, hospitals, construction sites, boardrooms… around the world – to catalyze scientific thinking at scale.

I’m not sure how one would go about trademarking ‘scientific thinking’ as this is  a very commonly used phrase and I’m pretty sure a case could be made that it has been common language for centuries.  This oddity had me going back to the Visualizing.org for their terms and conditions, which are largely unexceptionable,

These are the general terms of use. For terms and conditions regarding the uploading of work, please read the Visualization Submission Agreement.

This Web site is owned by General Electric Company (“GE”) and operated by Seed Media Group, LLC (“Seed”). Throughout the site, the terms “we,” “us” and “our” refer collectively to GE and Seed. We offer this Web site, including all information, tools and services available from this site, to you, the user, conditioned upon your acceptance of all the terms, conditions, policies and notices stated here. Your use of this site constitutes your agreement to these Terms of Use.

…

When you submit material other than a Visualization, you grant us and our affiliates an unrestricted, nonexclusive, royalty-free, perpetual, irrevocable and fully sublicensable right to use, reproduce, modify, adapt, publish, translate, create derivative works from, distribute and display such material throughout the world in any media. You further agree that we are free to use any ideas, concepts, know-how that you or individuals acting on your behalf provide to us. [emphasis mine] You grant us and our affiliates the right to use the name you submit in connection with such material, if we so choose. All personal information provided via this site will be handled in accordance with the site’s online Privacy Policy. You represent and warrant that you own or otherwise control all the rights to the content you post; that the content is accurate; that use of the content you supply does not violate any provision herein and will not cause injury to any person or entity; and that you will indemnify us for all claims resulting from content you supply.

Interesting, non? This has me wondering if it’s possible that  these folks (GE & Seed Media) might decide to use a concept from the visualization without any permission needed. If I understand this rightly, the promise is the visualization won’t be used, all they need is the idea or concept and either company (GE/Seed) or their affiliates can find someone else to illustrate or visualize it.  I find a company (Seed) that’s trying to trademark ‘scientific thinking’ might have some credibility issues regarding their stated terms and conditions for this visualizing.org website.

For the icing on this visualization cake, here’s a video from Visualizing.org’s About page where there is much discussion about the importance of design and visualization of data but not one single scientist is featured,

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Policy visualization tool

Monday, December 3rd, 2012

Thanks to David Bruggeman and his Dec. 2, 2012 posting on the Pasco Phronesis blog for this information about a very intriguing project, a policy visualization tool,  (Note: I have removed links),

ProjectPolicy.org is a startup effort established by a team of Cambridge researchers working to make it easier to access policy-relevant data.  …

They are looking for help, and are advertising for Policy Fellows and a Technology Associate. The Policy Fellows would work remotely, gathering and curating data for a particular geographic region.

I found more information about ProjectPolicy in a Nov. 23, 2012 University of Cambridge news release,

The winning project of the SVC2UK Cambridge Startup weekend, which took place at Cambridge Judge Business School between 9 and 11 November 2012, has gone on to win the Grand Finale in London.

ProjectPolicy.org is an online, intuitive tool to help make sense of policy information by aggregating data from different sources. Following a pitch by Nathan Boublil and Agastya Muthanna, the team behind ProjectPolicy was formed during the SVC2UK Cambridge Startup Weekend and together the five team members developed and presented the initiative as a viable business opportunity to a panel of judges.

This project is currently one of 15 semi-finalists in the Global Startup Battle which hosted 138 teams battling for a spot in the semi-finals. The online battle was waged from Nov. 9 – 19, 2012 (over two weekends) with 10,000+ participants in 100+ cities around the world. Here’s some information about the panelists currently judging the semi-finalists’ project in a Nov. (?), 2012 posting on the SW blog (Note: I have removed links),

TONY HSIEH 

In 1999, at the age of 24, Tony Hsieh sold LinkExchange, the company he co-founded, to Microsoft for   $265 million.

He then joined Zappos as an advisor and investor, and eventually became CEO, where he helped the company grow from almost no sales to over $1 billion in gross merchandise sales annually, while simultaneously making Fortune magazines annual Best Companies to Work For list. In November 2009, Zappos.com, Inc. was acquired by Amazon.com in a deal valued at $1.2 billion on the day of closing.

BRAD FELD

Brad is one of the managing directors at Foundry Group, a venture capital firm that invests in early stage software / Internet companies throughout the United States. He is also the co-founder of TechStars, a mentor-driven accelerator, author of several books and blogs, and a marathon runner.

Brad has been an early stage investor and entrepreneur since 1987. Prior to co-founding Foundry Group, he co-founded Mobius Venture Capital and, prior to that, founded Intensity Ventures, a company that helped launch and operate software companies. Brad is also a co-founder of TechStarts.

…

LEAH BUSQUE

A true visionary, Leah Busque (@labusque) is the founder and chief executive officer of TaskRabbit.com, an online marketplace where you can outsource small jobs and Tasks to others in your own community. TaskRabbit is the pioneer in “service networking” – a concept Leah conceived and has since evangelized. Now an industry-wide concept, service networking describes the productive power of a web-based, social-networked community.

Since its founding in 2008, Leah has grown TaskRabbit to more than 40 employees and has expanded the service to Boston, Chicago, Los Angeles, New York City, Portland, San Francisco, and Seattle with several more markets to come in 2012. Under her leadership, TaskRabbit was named one of the “Next Big Things in Tech” by WSJ Digits, Start up to Watch in 2012” by Inc. Magazine, and a finalist for “Mobile app of the year” in 2011 by both the Crunchies and Mashable Awards.

CHRIS HOLLOD

Chris Hollod lives in LA and works directly with Ashton Kutcher, Guy Oseary, and Ron Burkle to help manage their venture capital fund, A-Grade Investments.

Chris’s responsibilities include evaluating new opportunities, managing deal flow, spearheading the investment process, executing deals, and coordinating with portfolio companies.

Chris also works as an Associate for The Yucaipa Companies, a private equity firm founded by Ron Burkle.  Prior to joining A-Grade Investments and The Yucaipa Companies, Chris worked in Investment Banking.  Chris graduated summa cum laude and Phi Beta Kappa from Vanderbilt University with a degree in Economics and minors in Finance and Philosophy.

JESSE DRAPER

Jesse Draper is creator and host of “The Valley Girl Show” through which she’s become a spokesperson for startups and helped pioneer the way of new media content distribution.

Formerly a Nickelodeon star, Draper is now CEO of Valley Girl™ where she runs pre-production through post-production and distribution for the show, runs technology blog Lalawag.com and is a regular featured writer for Mashable, San Francisco Chronicle, Huffington Post and Glam. Draper is also a speaker at business conferences around the world including DLD, SXSW and universities such as Stanford.

Getting back to ProjectPolicy.org, there’s more information in a brief video they’ve produced,

If you are interested in helping this team make its policy visualization tool useful and accessible, here’s more about the positions they are advertising,

As a Technology Associate, you will help the technology team develop the platform.

You will be responsible for helping to develop crucial modules of the product. This

will be a valuable learning opportunity for you to work in product development at a

fast-growing startup. The fellowship can be part-time or full-time, carried out

virtually and alongside studies (Compsci/Engineering undergrad/postgrad or

other activities).

Duration: 3 to 6 months, depending on preference. Expenses reimbursed.

Joining date: ASAP

Requirements:

- Excellent Programming skills

- Knowledge of Web based Software development methodologies

- PHP

- MySQL

- Server side Java including Web Service development

- JavaScript

- Google Maps API

- Google Fusion Tables

- Software Testing

- Ability to learn new technologies

- Willingness to work independently

- Organised.

To apply, please email your CV and a short paragraph explaining your motivations

and why you want to join us to: contact@projectpolicy.org

As a Policy Fellow, you will work remotely to assist the team in developing the first
online platform focused on public policy. Responsible for a geographic area you
will assist in data selection and curation at the local level.
As an Economics/Politics/Public Policy/International relations student or recent
graduate, you must be familiar with researching quantitative and qualitative
information quickly and accurately.
We are currently looking for Policy Fellows to cover the following territories:
- North America;
- Asia (with fluency in relevant languages);
- Continental Europe (with fluency in relevant languages);
- Spain and South America ex Brazil (fluency in Spanish required);
- Portugal and Brazil (Fluency in Portuguese required);
- Sub-saharan Africa (with fluency in relevant languages).
Policy Fellows are expected to work independently and virtually.
Duration: 6 months min.
Joining date: ASAP.
Time commitment: 4-6 hours per week.
To apply, please email your CV and a short paragraph explaining your motivations,
area of interest and why you want to join us to: contact@projectpolicy.org

I wish ProjectPolicy.org good luck in the competition and I hope to be seeing their tools online in the near future.

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Mapping geographies of the planet and of ourselves

Tuesday, September 11th, 2012

Why are there so many maps? We’re mapping our brains; various genomes; fantasy and literary environments; with increasing granularity, our cities (thank you, Google); and more, both on and off the planet.

The urge of map something or anything is old, stretching back at least 8,000 years (according to the History of Cartography essay on Wikipedia) and it spans various cultures, Arab, Chinese, Indian, European, Mongolian, and others .

We seem compelled to create maps as a means of understanding and exploring our planet, ourselves, and more. Lately, it seems there’s been a ‘mapping explosion’ and I’m not the only one to notice.  Brian Timoney in a Sept. 1, 2011 posting on Mapbrief.com comments,

That the web mapping explosion of the past few years has ushered in a new Golden Age of Cartography has been noted more than once (here, here, and here). But what is really exciting is that the increasing variety of tools for map-making are engaging folks from a variety of disciplines, including the emerging field of Information Design. For those of us with traditional GIS training, the delight of encountering great cartography in unexpected places is tempered by the realization that while we GISers are good at making maps, we seem especially adept at making ugly maps.

…

…, why does any of this matter? Because good design enhances comprehension.  As the stories we are trying to tell with maps become more multivariate and nuanced, the penalty for thoughtless design is at best puzzlement, at worst misunderstanding. We have arrived at a point where the ‘general user’ does notice the difference in cartographic presentation between Google Maps, Bing, Mapquest, and Open Street Map.

As per my mention of brains and genomes (human, bacteria, plant, etcl) earlier, scientists seem to have discovered a new passion for mapping.

Strangely, we don’t tend to remember that all maps are inaccurate; they are only approximations. This is certainly not mentioned in this BBC (British Broadcasting Corporation) produced short video from Episode 3 of the Beauty of Maps, which extolls what’s described as a golden age of cartography in Amsterdam,

I wonder how the practice of science is going to change as we map and visualize data with more frequency and the written word loses its primacy.

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Islands of Benoît Mandelbrot: Fractals, Chaos, and the Materiality of Thinking exhibition opening in Sept. 2012 in New York

Monday, September 3rd, 2012

What a fabulous idea! The Bard Graduate Center for Studies in the Decorative Arts, Design, and Culture is holding an exhibit of Benoit Mandelbrot’s images from Sept. 21, 2012 – Jan. 27, 2013 in New York City (from the July 31, 2012 announcement)

The Exhibition

Focusing primarily on the work of Benoît Mandelbrot (1924–2010), one of the most notable mathematicians of the twentieth century, this exhibition explores the role of images in scientific thinking. With their capacity to generate and shape knowledge, images are at the very core of scientific investigation: charts, graphs, notebooks, instrument readings, technological representations, even mental abstractions–all make up the essential stuff of which it is made.

For thousands of years, Western thought assumed that the fundamental geometry of the world consisted of regular, ideal forms (cubes, spheres, cones, et cetera) with straight or evenly curved faces and edges. Benoît Mandelbrot, however, decided to explore the mathematics of the world not in its idealized form, but as it actually appears, in all its untidiness and irregularity, devoting himself to the study, for example, of the forms of the coastlines of real islands, with all their unpredictable inlets, creeks, and furrows.

Mandelbrot, in other words, looked at the world. In so doing, he flouted what was in effect a prohibition in much of mathematics against the use of visual representation in the discipline. To reintroduce the visual there, Mandelbrot took the step of harnessing the potential of computers, transforming mathematics into an experimental science. The result was his invention of fractal geometry, a geometry of actuality rather than of abstractions.

At his death in 2010, Mandelbrot left a mass of idiosyncratically organized drawings, computer print-outs, films, manuscript scribbles, objects, and photographs in his office in Cambridge, Massachusetts, an extraordinary trove to which Mandelbrot’s wife, Aliette, generously allowed Bard Graduate Center Visiting Assistant Professor Nina Samuel access. To explore it was like wandering through the mathematician’s brain—like witnessing the ephemeral traces of his very thought processes. Selections from these materials form the core of the exhibition.

Here’s a bit more about the exhibit and its curator from the undated press release,

Focusing primarily on the work of one of the most notable mathematicians of the twentieth century, The Islands of Benoît Mandelbrot: Fractals, Chaos, and the Mate­riality of Thinking, on view at the Bard Graduate Center from September 21, 2012 to January 27, 2013, explores the role of images in the development of what has become known as fractal geometry and chaos theory. Nina Samuel, a visiting assistant professor at the BGC, is the curator. Samuel, who received her PhD in art history from the Humboldt University of Berlin, is also an asso­ciate member of Das Technische Bild in Germany and a former member of the Swiss national research program eikones/NCRR Iconic Criticism.

…

“To explore it was like wandering through the mathematician’s brain,” said Samuel. “It was like witnessing the ephemeral traces of his very thought processes.” Selections from these mate­rials form the core of the exhibition.

Along with this rare look into Mandelbrot’s working process, sketches from his contemporaries—the French mathematician Adrien Douady and the German bio­chemist Otto E. Rössler—will also be publicly exhibited for the first time. The work of the Massachusetts Insti­tute of Technology meteorologist Edward N. Lorenz, a pioneer of chaos theory, will be represented by loans from the Library of Congress.

The writer has made some assumptions about the audience, from the press release,

The Islands of Benoît Mandelbrot: Fractals, Chaos, and the Materiality of Thinking allows the viewer to question the idea that the illustration of a work must always be secondary to the work itself. On the contrary, substantive images often play generative roles in the scientific pro­cess, constituting a kind of material thinking conducted by producing and interpreting visual traces, such as computer-generated images. These images are often aes­thetically compelling even if they are initially scientifical­ly impenetrable. This constitutes another revelation of the exhibition: the beauty of material thinking that can be found in the visual detritus of scientific investigation.

I think this exhibit is very much part of a trend towards re-examining how we create and organize ideas (scientific and otherwise) and, ultimately, how we think. I’ve a number of  commentaries in the ‘visual data’ category for this blog, the most recent being Big data, data visualization, and spatial relationships with computers, which I finished with this thought,

I think the real game changer for science  (how it’s conducted, how it’s taught, and how it’s communicated) and other disciplines is data visualization.

To whet your appetite for the ‘Islands of Benoit Mandebrot’, here’s an image from the exhibit,

Benoît Mandelbrot and Alan Norton. Computer graphic on photographic paper, 1983. Collection Aliette Mandelbrot.

There’s more information about the Mandelbrot exhibition on the event page including information about a book/catalogue being published, from the press release,

The Islands of Benoît Mandelbrot: Fractals, Chaos, and the Materiality of Thinking is accompanied by a fully illus­trated book with essays by Professor Samuel and mem­bers of the German research group Das Technische Bild—Matthias Bruhn and Margarete Pratschke—as well as scholars Wladimir Velminski, Jan von Brevern, and Juliet Koss. Drawing new connections between the material world and that of mathematical ideas, the publication offers not only a rare glimpse at the arti­factual terrain and graphic methodologies of Benoît Mandelbrot and his contemporaries but also investigates the role of scientific imagery in visual thinking across diverse disciplines. Published with Yale University Press (October 2012, paper, 160 color and b/w illustrations, 172 pages), it will be available for $40 in the BGC gallery and through the Web site (bgc.bard.edu).

I guess those of us who can’t attend will be able to enjoy the experience vicariously through the catalogue.

ETA Sept. 18, 2012: I knew Mandelbrot’s name was wrong somewhere in here. Sadly, I didn’t double check the headline till now.

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Big data, data visualization, and spatial relationships with computers

Friday, August 3rd, 2012

I’m going to tie together today’s previous postings (Sporty data science,  Digitizing and visualizing the humanities, and Picture worth more than a thousand numbers? Yes and no with a future-oriented Feb. 2010 TED talk by John Underkoffler (embedded below). I have mentioned this talk previously in my June 14, 2012 posting titled, Interacting with stories and/or with data. From his TED speaker’s webpage,

Remember the data interface from Minority Report? Well, it’s real, John Underkoffler invented it — as a point-and-touch interface called g-speak — and it’s about to change the way we interact with data.

…

When Tom Cruise put on his data glove and started whooshing through video clips of future crimes, how many of us felt the stirrings of geek lust? This iconic scene in Minority Report marked a change in popular thinking about interfaces — showing how sexy it could be to use natural gestures, without keyboard, mouse or command line.

John Underkoffler led the team that came up with this interface, called the g-speak Spatial Operating Environment. His company, Oblong Industries, was founded to move g-speak into the real world. Oblong is building apps for aerospace, bioinformatics, video editing and more. But the big vision is ubiquity: g-speak on every laptop, every desktop, every microwave oven, TV, dashboard. “It has to be like this,” he says. “We all of us every day feel that. We build starting there. We want to change it all.”

Before founding Oblong, Underkoffler spent 15 years at MIT’s Media Laboratory, working in holography, animation and visualization techniques, and building the I/O Bulb and Luminous Room Systems.

He’s talking about human-computer interfaces but I found the part where he manipulates massive amounts of data (from approx. 8 mins. – 9.5 mins.) particularly instructive. This video is longer (approx. 15.5 mins. as opposed to 5 mins. or less) than the videos I usually embed.

I think the real game changer for science  (how it’s conducted, how it’s taught, and how it’s communicated) and other disciplines is data visualization.

ETA Aug. 3, 2012 1:20 pm PDT: For those who might want to see this video in its ‘native’ habitat, go here http://www.ted.com/talks/john_underkoffler_drive_3d_data_with_a_gesture.html.

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Picture worth more than a thousand numbers? Yes and no

Friday, August 3rd, 2012

Shades of my Feb. 22, 2011 posting, No! A picture is not worth 1,000 words! There’s a July 26, 2012 news item on ScienceDaily titled, Picture worth more than a thousand numbers:: New Data Visualization Tool Helps Find the ‘Unknown Unknowns’,

A research team at the Georgia Tech Research Institute (GTRI) has developed a software tool that enables users to perform in-depth analysis of modeling and simulation data, then visualize the results on-screen. The new data analysis and visualization tool offers improved ease of use compared to similar tools, the researchers say, and could be readily adapted for use with existing data sets in a variety of disciplines.

…

“Data visualization supports data analysis by letting users pose data-related questions onscreen with ease and then view the answers in ways that go far beyond ordinary table formats,” said Edward Clarkson, a GTRI research scientist who is leading the data visualization work. “A picture can be worth a thousand numbers, because visualizing data in a graph allows us to see patterns that might not be apparent from purely numerical results.”

Here’s an example of what the tool can help researchers find,

Clarkson recently demonstrated the capabilities of the data analysis and visualization tool using an existing database: baseball statistics. This particular demonstration involved the use of 40 different data filters available onscreen; the TMT [Test Matrix Tool] system allows for 300 or more such filters.

In a random query of the 46,000 National League players from the past, an onscreen graph unexpectedly revealed an interesting anomaly during the demonstration. The data indicate that players’ height and weight increased in every past decade except the 1920s and 1930s, when it stayed inexplicably flat.

“That’s the beauty of this kind of tool — it can find the unknown unknowns,” Clarkson observed. “Details show up in graphs that aren’t obvious when you’re looking at just the numbers.”

I’m not sure I find that statistic to be a compelling example of an ‘unknown unknown’  that said I do find this trend toward visualizing data is getting more pronounced. I have another recent item on data visualization in my July 12, 2012 posting of the DAVinCI system at Rice University.

As for my 2011 posting on words and images, that too was about data visualization. I was pointing out the glibness of the saying, ‘A picture is worth a 1000 words.’  Sometimes, it isn’t. The trick lies in making the most effective choice for the situation.

You can find the July 26 (?), 2012 case study (which originated the news item) on the Georgia Tech Research Institute website.

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Visualizing 20 atoms of gold

Wednesday, August 1st, 2012

For an outsider it seems like an odd thing to do, theorize about how atoms of gold and other elements might be arranged. I assume this is why there are people who like to write and people (physicists and others) who like to theorize about atoms. The July 26, 2012 news item on Nanowerk notes that a theory about gold atoms has been successfully visualized at the University of Birmingham , UK (Note: I have removed a link),

Scientists at the University of Birmingham have developed a method to visualise gold on the nanoscale by using a special probe beam to image 20 atoms of gold bound together to make a cluster. The research is published today (26 July 2012) in the Royal Society of Chemistry’s journal Nanoscale (“Direct atomic imaging and dynamical fluctuations of the tetrahedral Au20 cluster”).

This is the part of the story I found rather interesting (from the University of  Birmingham’s July 19, 2012 pre-released news item ,

Physicists have theorised for many years how atoms of gold and other elements would be arranged and ten years ago the structure of a 20-atom tetrahedral pyramid was proposed by scientists in the US. Birmingham physicists can now reveal this atomic arrangement for the first time by imaging the cluster with an electron microscope.

Here’s the image the scientists have produced,

A cluster of twenty atoms of gold is visualised for the first time by Birmingham physicists

The work is not entirely devoted to theory (from the pre-released news item),

Richard Palmer, the University of Birmingham’s Professor of Experimental Physics, Head of the Nanoscale Physics Research Laboratory, and lead investigator, said: ‘We are working to drive up the rate of production of these very precisely defined nano-objects to supply to companies for applications such as catalysis. Selective processes generate less waste and avoid harmful biproducts – this is green chemistry using gold.’

I’m not sure how you go from a 20-gold-atom tetrahedron to driving up the rate of production, so I’m hoping to hear more about this in the future.

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DAVinCI lets Rice University researchers visualize their data big time

Friday, July 13th, 2012

The July 13, 2012 news item on physorg.com presents an extraordinary picture (Note: I have removed a link),

The 200-inch wall (measured diagonally) lets users display and analyze images of all types, from atoms to galaxies. This studio is expected to help researchers in Earth science, biomedicine, engineering, art, architecture and other fields gain extraordinarily clear pictures of their data sets, be they bacteria or bridges.

“I can take my 3-D seismic images,  project them here and walk around inside them,” said Alan Levander, Rice’s Carey Croneis Professor of Earth Science and principal investigator of the Data Analysis and Visualization Cyberinfrastructure (DAVinCI) project. “With a tracking device in my hand, I can go through and choose the features that I want to look at.” The DAVinCI project adds to Rice’s extensive supercomputing resources, which also include Blue Gene/P, among the 500 most powerful supercomputers in the United States.

The news item originated in a July 12, 2012 Rice University news release by Mike Williams,

The futuristic wall of 50-inch high-resolution projection monitors supports two- and three-dimensional visualization needs at extremely high resolution and clarity, Odegard [Jan Odegard, executive director of Rice’s Ken Kennedy Institute for Information Technology] said. Backed by custom graphics engines, the wall allows data to be displayed in three dimensions using modern active stereo shutter glasses, often seen in home 3-D TV systems but far more sophisticated than glasses used at a 3-D movie theater.

The shutters are linked wirelessly to the graphic engines so that, in effect, only one eye is open at a time, and it matches the left or right images displayed on the screen. But this all happens very fast, at a frame rate of 120 times a second, so users see no flicker in their images.

Erik Engquist, manager of the lab who joined Rice last year, has been demonstrating the system with geological, molecular and other 3-D data that float in front of the screen and allow viewers to see details that might be invisible on flat images, no matter how big. The system has two other advantages over standard 3-D displays. The 32-megapixel screen can track researchers with an infrared system (also tied into the glasses) and allows them to walk around inside an image. Researchers can also interact with the data by turning them this way and that in midair to get a different perspective and interpret the data quantitatively.

“If you have a 10-dimensional data space — which is not uncommon — you can’t visualize it in 10 dimensions, but you can visualize any three at a time,” Levander said. “You can walk through complicated multidimensional space looking at what are called ‘hypercubes.’ You can interact with them and look for correlations in complex systems.”

Engquist, an applied mathematician, said the 16 projection monitors were chosen for their display brilliance and their narrow borders that leave only a thin strip of black between individual screens. “It’s far less intrusive than if we had used regular TV monitors, which have a large bezel,” he said. “If the images have a black background, you barely see the lines; in fact, after a while you don’t really notice them, since your focus will be on the data.”

Here’s a video about DAVinCI produced by Rice University,

The official opening for this project is Sept. 5, 2012 but researchers are already working with this new equipment (or playing with a fabulous new toy which brings to mind the Star Trek holodeck). Rice University has made an online technical manual, Getting Started on DAVinCI available. You need to be familiar with the Linux operating system and comfortable with writing short scripts (i.e., have rudimentary programming skills).

 

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Teaching physics visually

Wednesday, May 23rd, 2012

Art/science news  is usually about a scientist using their own art or collaborating with an artist to produce pieces that engage the public. This particular May 23, 2012 news item by Andrea Estrada on the physorg.com website offers a contrast when it highlights a teaching technique integrating visual arts with physics for physics students,

Based on research she conducted for her doctoral dissertation several years ago, Jatila van der Veen, a lecturer in the College of Creative Studies at UC [University of  California] Santa Barbara and a research associate in UC Santa Barbara’s physics department, created a new approach to introductory physics, which she calls “Noether before Newton.” Noether refers to the early 20th-century German mathematician Emmy Noether, who was known for her groundbreaking contributions to abstract algebra and theoretical physics.

Using arts-based teaching strategies, van der Veen has fashioned her course into a portal through which students not otherwise inclined might take the leap into the sciences — particularly physics and mathematics. Her research appears in the current issue of the American Educational Research Journal, in a paper titled “Draw Your Physics Homework? Art as a Path to Understanding in Physics Teaching.”

The May 22, 2012 press release on the UC Santa Barbara website provides this detail about van der Veen’s course,

While traditional introductory physics courses focus on 17th-century Newtonian mechanics, van der Veen takes a contemporary approach. “I start with symmetry and contemporary physics,” she said. “Symmetry is the underlying mathematical principle of all physics, so this allows for several different branches of inclusion, of accessibility.”

Much of van der Veen’s course is based on the principles of “aesthetic education,” an approach to teaching formulated by the educational philosopher Maxine Greene. Greene founded the Lincoln Center Institute, a joint effort of Teachers College, Columbia University, and Lincoln Center. Van der Veen is quick to point out, however, that concepts of physics are at the core of her course. “It’s not simply looking at art that’s involved in physics, or looking at beautiful pictures of galaxies, or making fractal art,” she said. “It’s using the learning modes that are available in the arts and applying them to math and physics.”

Taking a visual approach to the study of physics is not all that far-fetched. “If you read some of Albert Einstein’s writings, you’ll see they’re very visual,” van der Veen said. “And in some of his writings, he talks about how visualization played an important part in the development of his theories.”

Van der Veen has taught her introductory physics course for five years, and over that time has collected data from one particular homework assignment she gives her students: She asks them to read an article by Einstein on the nature of science, and then draw their understanding of it. “I found over the years that no one ever produced the same drawing from the same article,” she said. “I also found that some students think very concretely in words, some think concretely in symbols, some think allegorically, and some think metaphorically.”

Adopting arts-based teaching strategies does not make van der Veen’s course any less rigorous than traditional introductory courses in terms of the abstract concepts students are required to master. It creates a different, more inclusive way of achieving the same end.

I went to look at van der Veen’s webpage on the UC Santa Barbara website to find a link to this latest article (open access) of hers and some of her other projects. I have taken a brief look at the Draw your physics homework? article (tir is 53 pp.) and found these images on p. 29 (PDF) illustrating her approach,

Figure 5. Abstract-representational drawings. 5a (left): female math major, first year; 5b (right): male math major, third year. Used with permission. (downloaded from the American Educational Research Journal, vol. 49, April 2012)

Van der Veen offers some context on the page preceding the image, p. 28,

Two other examples of abstract-representational drawings are shown in Figure 5. I do not have written descriptions, but in each case I determined that each student understood the article by means of verbal explanation. Figure 5a was drawn by a first-year math major, female, in 2010. She explained the meaning of her drawing as representing Einstein’s layers from sensory input (shaded ball at the bottom), to secondary layer of concepts, represented by the two open circles, and finally up to the third level, which explains everything below with a unified theory. The dashes surrounding the perimeter, she told me, represent the limit of our present knowledge. Figure 5b was drawn by a third-year male math major. He explained that the brick-like objects in the foreground are sensory perceptions, and the shaded portion in the center of the drawing, which appears behind the bricks, is the theoretical explanation which unifies all the experiences.

I find the reference to Einstein and visualization compelling in light of the increased interest (as I perceive it) in visualization currently occurring in the sciences.

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Posted in science, Visual Art, visual data | 1 Comment »

Science images too busy/ugly? Call the University of Washington’s Design Help Desk

Wednesday, February 22nd, 2012

After several days at the AAAS (American Association for the Advancement of Science) 2012 annual meeting, I can definitely support the design help desk project at the University of Washington (UW). From the Feb. 22, 2012 news item by Hannah Hickey on physorg.com,

A group of University of Washington researchers has launched a unique experiment matching science students with those in design. The new Design Help Desk, similar to a writing help desk, offers scientists a chance to meet with someone who can help them create more effective figures, tables and graphs.

“In modern publications, up to half of the space can be taken up by figures,” said principal investigator Marco Rolandi, a UW assistant professor of materials science and engineering. His group studies materials at the nanometer scale, and much of the data is ultimately contained in microscope images.

“As a new faculty member, I was spending a lot of time teaching my students how to make figures for publications, even though I myself didn’t have any formal training,” Rolandi said.

It was a case of the blind leading the blind, he said. Rolandi sought out collaborators on campus, and eventually funding from the National Science Foundation, to create support that until now didn’t exist – and to study how well it works.

The research project (Design Help Desk) has two principal investigators, Rolandi and Karen Cheng, from Hickey’s Feb. 21, 2012 news release on the University of Washington website,

“We are becoming a more visual culture,” says Karen Cheng, a UW associate professor of design (who also completed a bachelor’s in chemical engineering). Still, most science visuals “could use significant improvement from a visual point of view,” she said. “It’s just not a field where design has been part of the training.”

This hasn’t always been the case. In Galileo’s time, scientists were also trained in art. These days, scientists often produce a graph using Microsoft Excel or PowerPoint’s default settings – which might look fine to them, but may have fundamental design problems. [emphasis mine]

Meanwhile, even journals are focusing on the importance of figures, often asking authors to improve them before publication.

“It’s not just about looking pretty. It’s about conveying complex information in a clear way,” Cheng said.

The point about science and art being more closely intertwined in the past was made Gunalan Nadarajan (Vice Provost at the Maryland Institute College of Art) at the AAAS 2012 annual meeting (my Feb. 20, 2012 posting). Nadarajan mentioned a new project being developed, Network for Science Engineering Art and Design. It’s so new they don’t yet have a website.

This is not being done in the wild. Scientists and designers are not set loose upon each other (from the UW news release),

Clients who arrive for a session at the Design Help Desk are first greeted by postdoctoral researcher Yeechi Chen, who earned her doctorate in physics at the UW and has completed a UW certificate course in natural science illustration. Chen can act as an intermediary between the scientist and the designer, and reassure new clients that scientists are involved in the project.

During the half-hour session, the scientist client and design consultant are alone in the room. The designer first asks the scientist about his or her goals – timeline, stage in the design process, publication venue, and main points to convey. The designers typically use pen and paper to sketch out their ideas.

The session is videotaped for use in the group’s study, if the client agrees. One camera records the face-to-face interaction, while a second camera on the ceiling records the sketching and hand movements.

Interestingly (to me anyway), the Design Help Desk appears on a UW webpage dedicated to Visual Communication in {Nano} Science. The page offers a very minimalist image, a description of the project and the team, and offers links to resources, e.g., A Brief Guide to Designing Effective Figures for the Scientific Paper ((behind a paywall)) which was published  in August 2011 in Advanced Materials.

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Posted in nanotechnology, science communication, visual data | 1 Comment »

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