Author: Sonia Stephens

Categories
bunny

Friday bunnyblogging

My recent blogging hiatus comes from a very needed vacation that ended up being more vacationy than expected. I’ll write more about hiking in future posts… Currently a bit jet-lagged, but wanted to post something about Noe, who was mostly good while we were gone.

petting Noe
It's about time you got back...

While Noe has an excellent bunnysitter who comes over twice a day, she still gets bored and destructive. This time, apparently she got into some of my bank statements, which were foolishly in her reach (but which had never been interesting before,) and ate the tassels off of a small carpet in the kitchen. At least the latter seems to have caused her no ill effects, the idiot. She seems not to have destroyed any pillows or carpet or managed to get up onto the dining room table, so that’s nice…

But now she is all about the forehead rubs. And parsley.

Categories
bunny

Friday bunnyblogging

A bored bunny is a destructive bunny. I’ve always thought that Noe would make an excellent paper-shredder. Who needs one of those fancy machines when you have your own furry agent of entropy on hand?

I can haz entropy?

The second law of thermodynamics states that spontaneous natural processes increase the entropy of a system. Rabbits are excellent at creating disorder. They are little entropy machines, taking plants, chopping them up, compacting the remains into little balls, and extracting energy to use for destruction. If she was a D&D character, she would be chaotic neutral.

This took place in about an hour one day, when she was feeling especially frenetic. We no longer keep old newspapers where she can get to them. It’s apparently great fun, but really a pain to clean up.

Categories
bunny

Friday bunnyblogging

In my last bunny post, I mentioned Noe’s “bunny palace:” a bike box cut in half and stacked with another box to make a 3-level structure. You can see only two levels in this photo, but here it is. There’s a smaller box on top, but it’s cut off in this photo.

Notice that the levels are perfect bunny-height: tall enough to hop around in, but short enough for a tunnel-like feel.

Here she is on level 2, munching on hay:

Having several entrances into each level is a must.

You can also buy specially-made cardboard bunny houses, but my philosophy is, as long as you have a pet that loves to play with old boxes, you should make the most of one inexpensive option.

Categories
bunny

Friday bunnyblogging

Noe loves cilantro.

NOM!

It is a tasty treat.

I will eat this one too.

One of her favorite veggies.

I see you have more over here...

She always suspects that we’re hiding just one more piece.

Let's see both hands, mister!
Categories
birds information representation visuals

Visualization project post, part 2

Because this was a very preliminary study, I only had 9 participants, mainly fellow students in the T&T program (and a last-minute addition of some family members). My main goal was to see if this would actually work, and I wasn’t really expecting dramatic results. Which is what happened- generally, there weren’t significant differences in the maps that the interactive and non-interactive viewers drew. This probably happened because the description of how to read a phylogenetic tree was too thorough (which, unfortunately, I realized after the fact…). If I do something like this again, I’ll definitely make this orientation info less detailed.

Overall, there were big differences in how well people remembered the two big groups on the tree- land birds and shorebirds- shorebird families were apparently much more challenging to remember. This result was correlated with how well people reported that they know birds in general: more general bird knowledge was related to doing better at remembering the shorebird part of the tree. One thing I might do differently would be to give people a list of family names- that way, at least terminology wouldn’t be an issue.

Some open-ended questions that I asked gave me more useful ideas for designing a future study. For example, several people said that they learned that specific families were related, but wanted to see more information on either the names of the branch groupings, or the common ancestor of related species. This raises a few interesting points, because higher-order taxonomy is often different than genetic differences (so there aren’t necessarily names for branches), and ancestral species are really hypothetical last common ancestors, not known species. It would be interesting to think of ways to communicate this to people in a diagram like this.

So, the upshot is that this project gave me some new ideas about how to design a study like this, even though it didn’t give me very conclusive results. Obviously, just adding interactivity to a phylogenetic tree won’t magically make people learn it better- it would be surprising if it did.

I probably won’t be working in interactive phylogenetic trees for my dissertation- there are a number of people working on that at the moment, but I’m think of working on something related. I’m sure I’ll be talking more about that here as my ideas come into shape.

For those interested: here’s the list of references I used in this project:

  • Baum, David A., Stacey D. Smith, and Samuel S. S. Donovan. “The Tree-Thinking Challenge.” Science 301 (2005): 979-980. Web.
  • Baum, David A., and Susan Offner. “Phylogenies and Tree-Thinking.” The American Biology Teacher 70.4 (2008): 222-229. Web.
  • Carrizo, Savrina F. “Phylogenetic Trees: An Information Visualisation Perspective.” Yi-Ping Phoebe Chen, ed. Conferences in Research and Practice in Information Technology 29 (2004): 315-320. Web.
  • Cranfill, Ray, and Dick Moe. Deep Green-Hyperbolic Trees. Web. 20 September 2010.
  • Liu, Zhicheng, Nancy J. Nersessian, and John T. Stasko. “Distributed Cognition as a Theoretical Framework for Information Visualization.” IEEE Transactions on Visualization and Computer Graphics. 14.6 (2008): 1173-1180. Web.
  • Maddison, David A, Katja-Sabine Schulz, and Wayne P. Maddison. “The Tree of Life Web Project.” Linnaeus Tercentenary: Progress in Invertebrate Taxonomy. Ed. Z.-Q. Zhang and W. A. Shear. Zootaxa 1668 (2007): 1-766. Web.
  • Rogers, Yvonne, and Mike Scaife. “How Can Interactive Multimedia Facilitate Learning?” In J. Lee, ed. Intelligence and Multimodality in Multimedia Interfaces: Research and Applications. Menlo Park, CA: AAAI Press, 1998. Web.
  • Scaife, Mike, and Yvonne Rogers. “External cognition: how do graphical representations work?” International Journal of Human-Computer Studies 45 (1996): 185-213. Print.
  • Stenning, Keith, and Jon Oberlander. “A Cognitive Theory of Graphical and Linguistic Reasoning: Logic and Implementation.” Cognitive Science 19.1 (1995): 97-140. Web.
  • Tree of Life Web Project. Web. 19 September 2010.
  • Tversky, Barbara. “Cognitive Maps, Cognitive Collages, and Spatial Mental Models.” A. U. Frank and I. Campari, eds. Spatial Information Theory: A Theoretical Basis for GIS, Proceedings COSIT ’93. Berlin: Springer, 1993. Print.
  • Yi, Ji Soo, Youn ah Kang, John T. Stasko, and Julie A. Jacko. “Toward a Deeper Understanding of the Role of Interaction in Information Visualization.” IEEE Transactions on Visualization and Computer Graphics 13.6 (2007): 1224-1231. Print.
  • Zhang, Jiajie, and Donald. A. Norman. “Representations in Distributed Cognitive Tasks.” Cognitive Science 18.1 (1994): 87-122.
Categories
birds evolution information representation visuals

Visualization project post, part 1

This semester, I worked on a small science visualization research project, partly for a course, and partly as a pilot study related to my possible ultimate dissertation research. I’ll probably break up my discussion of this project into a few posts.

I was interested in looking at whether interactivity affects people’s understanding of phylogenetic trees. Phylogenetic trees are one of the key tools used in the field of evolutionary biology to represent hypothesized evolutionary relationships among species or other biological groups. They let us both explore relationships among living species and make inferences about the history of life.

However, interpreting tree diagrams often presents a challenge to students. On trees, the nodes (branch points) symbolize the last common ancestor between the species represented by the branch tips. Inexperienced readers tend to “read” relationships along branch tips, rather than by nodes, which can lead to misconceptions like inferring that species on the tips gave rise to other species (e.g., frogs to snakes to birds). The correct way to read phylogenies is to think of the nodes as focal points that connect related species.

One of the diagrams from the project introduction.

My experiment was designed to test whether making a phylogenetic tree diagram interactive, in such a way as to emphasize the importance of branch-point connections, would help people recall relationships more accurately when drawing the tree from memory. Cognitive theory suggests that interactive science visualizations could be useful for building understanding, because as we manipulate a visualization, we are able to generate slightly different viewpoints of it. We then put these points of view together into a mental model. A number of groups (e.g., here, here) have experimented with interactive trees, but in most of these projects, viewers interact with the tree by selecting branch tips in a higher-level tree, which takes them to a screen with a lower-level tree. With this type of navigation, the viewer effectively zooms in on a specific region of the tree, and the overall context for the tree is lost.

For this project, I created a tree of Florida bird families, based on the information on the Tree of Life website. To help people with unfamiliar families, there was a thumbnail photo of a representative species and a short fact about each family on the tree.

Viewers could click on a node to "open up" a branch.

Viewers were presented with a complete tree (so they didn’t lose the overview of the entire tree), and had the ability to select one node with its connected species to highlight at one time (thus maintaining the importance of reading by nodes).

Example of an "open" branch.
The overall non-interactive tree. All photos open-source from Wikipedia.

My experiment worked like this: 1) viewers read a description of how to read a phylogenetic tree, 2) they either interacted with a dynamic tree or viewed a static tree, 3) were asked to draw the tree from memory, and 4) answered some questions about themselves and the tree. They weren’t told ahead of time that they would have to draw the tree from memory. In my next post, I’ll talk about what actually happened…

Categories
bunny

Friday bunnyblogging: special gift guide edition

Time for a short gift-giving guide for the rabbit in your life! Don’t worry- some of these these are last-minute do it yourself ideas for the person who finds him/herself needing a bunny present on short notice.

'Tis the season...

1. Paper towel or toilet paper tubes (make sure you take any leftover paper bits off). These have several uses:

    • Great for chewing (they make a cool hollow noise). Plus you can wrap them around the legs of your chairs to keep bunny from gnawing on the furniture…
    • Put hay inside for bunny to pull out. Hiding a treat in the middle, like a piece of carrot, will make bun very enthusiastic about this one.
    • A fun game you can play with your rabbit is “ring stack”: cut the tubes up into 1″ rings, then stack several into a pyramid shape. Bunny will have fun knocking them down, and picking them up to toss. Then you can stack them up again. Repeat until one of you gets tired.

    2. Empty clean cardboard boxes. Also a number of uses:

    • Small ones (too small for your rabbit to fit into) can be closed and given as chew toys. Now loves chewing on box corners. I imagine there’s a satisfying “crunch” as she gets through the corrugated paper.
    • For boxes that bun can fit into comfortably, and has enough room to take a few steps and turn around, cut two or three holes in the box  on either side, big enough for him to get through easily. Close up the box. Long boxes make fun spaces to run through. You can put newspaper inside to encourage digging (be sure to check to make sure he’s not using this as a litterbox).
    • You can be creative with putting boxes together. For Noe, we’ve taken a bike box, cut it in two,  stacked the halves on top of one another, added a smaller box on top, and cut holes between the levels and on several of the sides. Instant 3-level “bunny palace”! This is a fun place for her to explore, nap in, and snack on hay.

    3. Paper bags. Fun to crawl into, and gnaw their way out of. Give your bunny a head start by making a small hole in the bottom of the bag, and then leaving in on its side on the floor.

    4. Hard plastic toys- pet toys (balls with bells inside), baby toys (fake keychains are fun to toss), etc. Just make sure she’s not eating the plastic.

    5. Untreated straw balls and mats, and wicker balls. These are often available at specialist pet retailers and can be great fun to shred, roll, rip up, etc.

    6. Bunny-specific toys- these include things like dried cholla cactus and yucca rounds, wooden chew toys, and toys with bells that are fun to toss. There’s a huge variety out there- see the retailer links in #5 for ideas.

    Be sure NOT to let your bunny gnaw on treated wood, or any wooden toys that are dyed without food-grade dyes. If it’s apparent that she’s eating any plastic, replace the toy! For more toy ideas-as well as general bunny care tips- see the House Rabbit Society.

    Categories
    visuals

    Some notes

    A few comments:

    I’ve passed my third and final candidacy exam! Now, on to proposing a research project. I’ll certainly be talking more about that in the upcoming weeks…

    Today, I’ve added some portfolio items to this site. There’s also now a new “my portfolio” tab at the top. This includes some science visualizations, web-based projects, and excerpts from a few course papers. This has all been on another site up till this point, and I figured I should get it all in one place. The issue with some of the materials is that they’re pretty large visuals, so I’m trying to think of the best way to include it here. I’m a bit limited by the WordPress template, and will have to put some more effort into figuring out the best way to present this sort of material.

    I’ll be posting in the next few days about a semi-pilot (if that’s a real term) study on interactive science visualizations that I did this semester. What I wanted to look at was whether a specific type of interactivity in phylogenetic trees helps people learn relationships better than simply looking at a non-interactive diagram. More on that soon.

    Also, look for a special Friday bunnyblogging gift guide this week, for that special rabbit in your life!

    Categories
    bunny

    Friday bunnyblogging

    A cold front has just moved through Florida, leaving weather in the 60s in the daytime, and low 40s at night. It’ll be a while before we get any freezing temps (hopefully!), but it’s plenty cold for Noe.

    Nice and warm in the sun...

    She’s been exceptionally lazy the past few days, either laying in the sun or on ‘her’ chair under the dining room table. Possibly in part because her chair cushion has been reinforced with an old towel, after the foam eating incident a few weeks back. She seems to like the extra padding, too.

    My schedule is quite action packed, thank you very much.

    Usually, she will be more active in cold weather than in the heat- bunnies get overheated pretty easily- but ever since she developed arthritis, she’s been slow-moving the first few days it’s cold. We shall see how she acts over the winter.

    Oh, and she does still hop over to be underfoot in the kitchen, so we know all is well…

    Categories
    politics

    Personal information: who can you trust?

    In light of the outrage of Wikileaks’ release of classified government information, I would just like to relate two examples of cases where the government has screwed citizens over when it comes to their own privacy. Now, these examples are in no way comparable to more egregious breaches of citizen privacy by the government, but I think they do illustrate that assumptions of data privacy nowadays are pretty naive.

    Example 1: University of Hawaii
    In the past 6 months, University of Hawaii students and former students (like myself) have been informed twice that our personal information, including SSNs and possibly credit card information, has been breached twice. Part of the reason for this is that UH until very recently used students’ SSNs as identifying information in their databases, rather than student ID numbers. This means that, when coupled with basic data security incompetence, a whole slew of identifying information has apparently been available simply on the Internet because of UH-related screw-ups.

    The first incident involved a server at the Parking Office that was breached. 53,000 students, faculty, staff, and anyone who had a car towed on campus were affected. The second incident was more egregious: apparently a faculty member who was doing research on student records (including SSNs, names, dates, grades, academic history, etc.) “mistakenly” uploaded 40,000 student records onto the Internet. (The faculty member is now “retired”.) I suspect that this last breach may leave UH in violation of FERPA, which could mean serious fines.

    I’ve checked my credit records, and they’re fine, but I really have to wonder what steps UH is taking to upgrade their systems after these two incidents, now that they have a reputation for having crappy data-security policies.

    Example 2: State of Florida
    If the University of Hawaii is guilty of incompetence in a number of areas, it now appears that the state of Florida has been breaking federal privacy laws since 1995:

    …the state, specifically the Department of Highway Safety and Motor Vehicles, improperly sold personal information gleaned from about 31 million driver’s license records to Shadowsoft Inc., an Irving, Texas-based Internet marketer. Shadowsoft then sold the information to other firms that target consumers.

    …Such sales, however, violate a federal statute banning the disclosure of personal information from driver’s licenses, said Howard Bushman, an attorney with the Miami law firm representing the affected drivers. The information released included addresses, dates of birth and possibly Social Security numbers, Bushman said.

    Florida has no personal income tax. Therefore, it has high property taxes, lots of toll roads, and generally shitty public services (schools, public transport, etc.) It seems that another way the state has been making money has been by selling its citizens’ personal information to unspecified data miners. Over 31 million people have been affected by this practice. (It looks like other states may do it, too.) But hey- you can drive on the beach! Woo-hoo!

    …Oh, and just for more paranoia,  here’s another fun Florida story that suggests that you might be more at risk shopping at retail stores than online, just to add to the mix. Happy shopping!