Using the Flu as an Educational Opportunity

Illustration from David Macaluay's "The Way We Work", showing visitors throwing paper airplanes down air passages through the trachea.

Illustration from David Macaluay’s “The Way We Work”, showing visitors throwing paper airplanes down air passages through the trachea.

I woke up this Monday feeling sore, with a bad cough. Tuesday I barely had the energy to drag myself to a laptop to write this. It’s a familiar story for a lot of people around the United States right now, if the map at the top of this article is to be believed.

Yep, flu season is upon us in full swing, and in order to explain to my eight-year-old son what this means, I turned to that most awesome of all my medical reference books: David Macaulay’s The Way We Work. As you can probably guess from the title, this book provides a tour through all the major systems – circulatory, gastrointestinal, nervous, etc – that make up a human being, and contains several additional sections on health and disease. Like other David Macaulay books, including its more famous predecessor, The Way Things Work, David has meticulously illustrated the entire text with his colorful and quirky style. Diagrams of cross sections of tissue are visited by tiny tourists on observation platforms, schematics of biological systems are represented as bustling factories and conveyor belts, and sometimes even disembodied skeletons or diagrams of circulatory systems converse wryly with one another. My son eats all this up, and that’s good, as Macaulay’s light and humorous style comes with a serving of serious and well-presented content. I’ve always had a thing for the marriage of art and science, and this book is as good an example of this happy union as I can think of. Continue reading

Rocking Robotics With Kids and LEGO® Bricks

lego boysIf you happened to wander accidentally onto Madison College campus on the morning of Saturday November 9, you’d be excused for believing you’d stumbled into a giant middle school summer science camp. Teams of kids, aged anywhere between 7 and 14 wearing coordinated team t-shirts had the run of the place, putting finishing touches on their elaborate science project displays and robotic creations. Scattered across several locations around the campus, and providing a focus for the milling masses of hundreds of kids, their parents, coaches and spectators were several ping-pong sized tables, each one with an identically laid out obstacle course built entirely out of LEGO® bricks. From time to time a team of kids was summoned by a referee, and the real excitement began.

On getting a “thumbs up” from the team, the referee would set off a buzzer – the team, made up of anywhere from two to ten kids, would run up to the table. A couple of the kids set their robot – built around a LEGO® Mindstorms® “smart brick” – down nervously but quickly in a designated corner. One kid checked that the proper attachments to the robot were in place, the other verified that the right program was dialed in. They aligned their creation carefully on the table, and hit a big orange button on the body of the robot to launch it. The robot then trundled away – on wheels or treads depending on how the team conceived it – and pushed toy LEGO® trucks to designated zones on the board, wrecked some LEGO® buildings while carefully raising others above an imagined flood, rescued little LEGO® minifigs, and reunited LEGO® family members with each other and with their pets, also built of tiny LEGO®s. The robot returned to its home base as often as needed where the kids could tinker with it, switching out attachments and programs. Two and a half tense and breathless minutes after starting, the second buzzer sounded indicating the end of the round, and the team would erupt into a spontaneous cheer as its results were announced by the presiding judges.

Welcome to the annual BadgerLand Regional Tournament, a part of the FIRST® LEGO® League competition, one of many such events held across the world every year since 1998. Continue reading

Big Data Takes Education By Storm

weather blog

Gone are the days when the phrase “educational TV” would inevitably send shudders of dread through kids and teens. Quite the contrary, many of today’s educational programs are fast-paced, expertly narrated and full of surprising, fun, and visually engaging facts and science trivia. But while no doubt entertaining, are these programs still any good at their core function, namely teaching the kids actual concepts useful for understanding modern science?

The long-running PBS educational series, NOVA, aims to satisfy this goal by providing not only standard teachers’ notes and lesson plans to accompany its shows, but also by investing in extensive and realistic online laboratories in which students can explore actual scientific datasets. A good example of this approach is provided by the NOVA Cloud Lab, which is actually far more exciting than it sounds, as one of its main sections concerns the formation and study of storms. Continue reading

Vignettes From the Life of a Mobile Developer

Photo credit: https://www.flickr.com/photos/lincolnian/

Photo credit: https://www.flickr.com/photos/lincolnian/

To celebrate the release of iOS 7 and the new batch of iPhones, I’d like to share some highlights in the life of a mobile developer at Promega.

Promega was quick on the uptake when the iPhone was first released, and immediately spotted a unique opportunity to reach out to scientists in this new medium. A project quickly coalesced to create an iPhone app that combined the Protocols and Applications guide, easy access to our multimedia library, and the most popular Biomath Calculators. Promega thus made news as the first biotech company to release a resource-rich mobile app.

I, like many other developers, fell into writing code for smartphones and tablets almost by accident: When the iPad made its appearance in 2010, I was asked to see what it would take to make a version of the app for the then-brand new tablet from Apple.

As a freshly hired graphic designer with a background in computer science, I thought, I’d really just be creating the user interface for the tablet version of the app, and the programming can’t be all that involved, can it? The app’s already written, I’m just effectively re-potting it, right? Also, the practice of programming had changed significantly since my college days: documentation could easily be found online and extensive online communities of programmers, such as stackoverflow.com, now provide excellent peer support.

In spite of all this, the project proved more involved than I had anticipated. Continue reading

Of Primes, Fractals and Interactive Websites

spiral_primes1Warning: This blog post deals with mathematics, but not the math you may remember from school. But by virtue of it being mathematics, some people may be tempted to skip over this post. Don’t let this happen to you – there’s too much wonder here to miss out on.

Warning 2: The websites mentioned here use WebGL interactive 3D graphics: They only display correctly on browsers that support WebGL, such as Google’s Chrome browser. If you haven’t already done so, consider losing yourself for a few hours in the chrome experiments website.

Back when I was a mathematics graduate student in the early 1990’s, I felt that I had to sift through tomes of tedious formalism and obtuse notation to get at the few rare jewels of genuine mathematical insight. Or so my memory tells me. Then again, I also remember having to trudge uphill both ways through monstrous snow drifts to get to classes, so I can’t quite vouch for my memory (actually, that last part may have been somewhat true of the math department at the UW Madison, in the winter at least). In any case, my sense of mathematical wonder ebbed, and I eventually turned to the pursuit of more tractable goals, like finding a decent job and starting a family. In effect, I had built a mental wall between me and mathematics.

This wall only began to crack earlier this summer, when I saw a short but amazing presentation at the Eyeo festival in Minnesota. Continue reading

Analog is the new digital?

Photo credit: Niklas Roy https://picasaweb.google.com/116020019668259353077/CardboardComputerWorkshopAtHfGOffenbach#5847047713177417682

Playing “Speedway PRO 1000 at the Cardboard Computer Workshop” Photo credit: Niklas Roy

There are few areas of human endeavor as rife with error and retrospective hilarity as futurology, the dark art of predicting technological trends. So instead of trying my hand at proclaiming a new direction in human computer interactions, I thought I’d simply report on a couple of projects at the intersection of art and computing that caught my attention at the Eyeo Festival in Minneapolis, a visualization conference held there this past June. Perhaps there’s something more here than separate data points, but I’ll leave that inference up to the reader. Continue reading

The Stuff of Life: A genetics course in a comic book

Copyright by Mark Schultz, Zander Cannon and Kevin Cannon from “The Stuff of Life” (2009)

A few years back, when my wife and I were moonlighting as amateur comic artists, we would set up our table at local comic conventions. At one of these, we found ourselves sitting not too far from a charming comic artist by the name of Zander Cannon. His black-and-white artwork was gorgeous to behold. But what really drew us to him was a modest hardbound book on his table, entitled The Stuff of Life: A graphic guide to genetics and DNA that he co-illustrated with Kevin Cannon and whose script was written by Mark Schultz. It turns out that illustrating educational comics is one of Zander’s true passions. Of course, we bought our own copy. Continue reading

OneZoom, The Fractal Phylogenic Tree Explorer

OneZoom_zommed_out

I am reminded daily that we live in an age of wonders. To find out where somebody lives, I plug in their address into any one of a number of mapping web applications, and instantly see their neighborhood, detailed satellite views, driving directions, even gas stations nearby should I need to stop by one. I can similarly figure out who people are and how I’m connected to them with a variety of social networks, and all these data are delivered painlessly: No flipping through gargantuan phonebooks, no need for obscure incantations to formulate database queries.

Scientific visualization has been catching up in fits and starts to this new world of ubiquitous and trivially accessible relationship data. This is partly due to the inherent complexity of scientific data, and partly due to the vastly smaller user base that would benefit from such an endeavor, and the limited resources available to researchers. There are certain scientific datasets, however, that are eminently suited to benefit from this new visualization paradigm.

Consider the phylogenetic tree of living creatures: representing how different species are related to each other. Long ago in school, for example, I was taught that tetrapods (vertebrates, except for the fishes) were grouped into amphibians, reptiles, birds and mammals, pretty much in that order and with very little sense of how little or much diversity each of those groups encompassed. Since then, genetic sampling has revolutionized our understanding of the tree of life. However I’m pretty confident that kids are still taught about amphibians, reptiles, birds, and mammals, in pretty much that order. Perhaps somebody mentions that the dividing lines aren’t quite as clear-cut anymore, but that probably just muddles things even more.

James Rosindell and Luke Harmon took on this problem of visualizing the modern, genetics-based understanding of phylogeny in a way that is accessible to the general public. Their approach was inspired by the navigation conventions of Google maps, and by the aesthetics of fractals, especially the tree-like L-systems. Continue reading

Bacterial transformation and counting colonies for grade school students

Our experimental setup: Microbe plushies, Lego DNA, plates, iPhones and makeshift stand, ready to go.

Our experimental setup: Microbe plushies, Lego DNA, plates, iPhones and makeshift stand, ready to go.

A few weeks ago, our elementary school held its annual science fair. Owing to the greater-than-usual number of scientists among the parents, the halls of this event were lined with tables staffed by said parents, showing off the wonders of science, tech, and especially biotech. There were at least three stations devoted to various aspects of stem cell research, and the table next to us had kids run simple nucleic acid extractions from wheat germ using detergent and alcohol – my son loved that one, as he pulled out the stringy goop with a q-tip at the end of the process.

My wife and I contributed to the festivities by putting together a presentation on bacterial transformation. I was just about finished working on a colony counter iPhone® app for Promega, so I figured why not try it out in the field: Print out some colorful ersatz bacterial plates, have the kids count the colonies using the app (yay, touch screens!) and maybe teach them something about genetic engineering along the way.

Our setup turned out to be a lot of fun to run, and quite popular to boot. It went roughly like this: Continue reading

AutoPACK Visualization Challenge

HIV 3D structure in Blender, as imported from autoPACK

HIV 3D structure in Blender, as imported via autoPACK

Last week I attended VIZBI 2013, the 4th international conference on visualizing biological data. I was wowed by the variety of visualization techniques and tools presented, as well as by the high quality of art and design I saw on display . The conference covered a diverse range of visualization problems, from pure data visualizations of genomic, expression and even epidemiological data, to renderings of biological structures at various scales.

One of the posters presented at the conference that really impressed me showed off the entries for a contest, just finished, to render artistic visualizations of HIV in blood serum.
Continue reading