Author: Maciek Smuga-Otto

OneZoom, The Fractal Phylogenic Tree Explorer

Posted on by Maciek Smuga-Otto

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 “OneZoom, The Fractal Phylogenic Tree Explorer”

Bacterial transformation and counting colonies for grade school students

Posted on by Maciek Smuga-Otto

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 “Bacterial transformation and counting colonies for grade school students”

Science in the Service of Art

Posted on by Maciek Smuga-Otto

Three artists who use science as their starting point.

Galapagos Rice-Rat from 'The Zoology of the Voyage of H.M.S. Beagle'. This media file is in the public domain in the United States. This applies to U.S. works where the copyright has expired, often because its first publication occurred prior to January 1, 1923.
Galapagos Rice-Rat from ‘The Zoology of the Voyage of H.M.S. Beagle’ This media file is in the public domain in the United States. This applies to U.S. works where the copyright has expired, often because its first publication occurred prior to January 1, 1923.

My recent blog conversation (blogversation?) with Michele about the book The Where, The Why and The How stirred me up to think some more about the topic of science-flavored art. That book was full of delightful examples of artists using science as their inspiration; however no matter the topic or style of art, the illustrations never strayed from _illustrating_ the science they referenced. Some were more fanciful than others, but none questioned their basic intent.

Now, in literature there’s an entire genre dedicated to “science flavored” writing that ultimately doesn’t serve to illustrate any actual science concepts. I’m speaking of Science Fiction, of course, and while some early entries in the SF canon erred on the side of scientific accuracy, later practitioners of the genre took great liberties with the science, always ensuring that it served their literary goal and not vice versa. I was raised on a steady diet of Stanisław Lem books, and probably as a result tend not to demand much realism from my fiction.

On thinking about it, I’m rather surprised that the same is in general not true of art.

Continue reading “Science in the Service of Art”

How Is a Molecular Biologist Like a Computer Programmer?

Posted on by Maciek Smuga-Otto

My wife, the molecular biologist, tells me she spends her days “at the bench” and “in the hood.” There, she works with cells, plasmids, RNA, enzymes and buffers, incubators, water baths, columns, gels, filters and spectrophotometers. She transfers various quantities of liquids into and out of plastics and glassware. At least, that’s what I understand when I ask her, “how was your day?”

I can’t really understand her fascination with all of this, but then I don’t have to: I’m an app developer, a programmer who designs and builds applications for smartphones and tablets. My work day consists of sitting in front of a laptop, cranking out code. There’s the occasional break afforded by meetings and presentations, writing up design documents, sketching out how a user interface might look like. Then it’s back to the computer, and programming.

But in spite of these differences, there is a critical aspect of my wife’s work that, whenever she speaks of it, I immediately recognize in my own professional life: We both rely extensively on kits and components, and doing so profoundly affects the way that we approach our jobs. Continue reading “How Is a Molecular Biologist Like a Computer Programmer?”