Planet Zone12

When I was an undergraduate, I found that university really wasn't living up to my expectations of stimulating, interesting people and ideas.

But today, I was totally living the academic dream.

We had a visit from a leading expert on ant behaviour. This wasn't about computer ant algorithms; she studies real live ants. We started off the day with her talk on the Turtle Ants she's been studying in Mexico, a talk filled with pictures of ants and paths and grad students on ladders pointing at the trees. A talk filled with speculation about behaviour and patterns and analogies to search in computer networks and bifurcation of biological trees. Over the course of the day, the group talked ants, bees, simulations on the computer and using robots, immunology, flu and t-cells in the lung, patterns and theories. It was the kind of conjunction of ideas from multiple disciplines where things were just clicking and questions and potential experiments started getting debated.

Biochemistry from my scientist parents, ecology and field work from Macoun Club, immunology from the above plus my own master's research, algorithms from math and CS... I was pretty proud of myself for knowing the jargon pretty much across the board and being able to keep up. I love that I'm with a group where seemingly disjoint backgrounds are consistently recognized as a huge advantage, and my own particular background fits right in.

I learned a bunch about ants and flu today. My notebook is filled with doodles of ants and cells doing stuff. Apparently turtle ants, since they have paths in the trees, sometimes get the paths broken when the wind blows, and the ants just back up and wait for the wind to blow the branches back so they can keep going. I learned that swine flu's replication rates in cells are a hundred times higher than avian flu (and ~20 times more than regular flu) but avian flu does other things to suppress immune response. I learned some about how T-cells get into the lungs and find infection despite the fact that they don't seem to move fast enough to explain how well we handle infection. And I got to watch people putting ideas together in ways that might result in using experiments in ants to try to explain things that would be much harder to test in the lungs, and so many ideas that probably just couldn't happen anywhere else.

So if you've been wondering why the heck I moved here despite the many downsides about the US/desert/altitude/regional poverty/city, etc.... this is why: Cutting edge research at the conjunction of biology, computing, and maybe a few fields besides. Even if I decide to do something else once my contract is played out, this has already been amazingly worthwhile, and with my own project starting to take shape, I'm pretty sure it's just going to get better!

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I should just rename my blog to “Jason Talks About Games Louis Dozois Makes” but he’s come up with another one, this time building a game in a weekend that subsequently won Ottawa Game Jam’s “Best Concept” category. Better yet – it’s free! You can download and print the Aion tiles and instructions from their Game Jam page and play it yourself!

I got a chance to play it a few times at lunch and thought it was a lot of fun! The idea is you put down tiles “domino-style” and try to build loops, competing against your opponent to finish them. It’s easy to pick up, plays fast (about 20 minutes), it’s cleverly strategic, and well balanced. I think young kids would have an easy time of this one, but adults will enjoy the brain-bending situations and risky strategies that come from trying to out-think your opponent’s next move.

You can play with paper pieces, but Louis’ set is printed on stickers and then stuck to fancy wooden tiles. Clever monkeys could do the same thing with some foam-core or cardboard and have a nice set of their own.

Snapped a picture looking out over the experimental farm through this morning’s rolling fog. Those are trees and a little shed. No horizon line, though – just white meeting white.

- Took an impromptu trip to the Bay Area this weekend. Bit expensive since we decided to do this on Tuesday, but otherwise quite feasible, which is good to know for future trips! Mostly hung out with the new parents and thus got to meet the new babies, which was fun.

- My first visitor to Albuquerque has scheduled her flight. Which means I now have a time limit on unpacking and prepping the house! To be fair, it's perfectly feasible for visitors to show up anytime now (the spare bedroom has bed, lamp, sheets, etc. and I'm using it as a quiet place to chill or have a nap where John won't disturb me) but I'm hoping this will provide the push to make the place nicer.

- I hated moving, but at least I culled my stuff before I did. Not only does it suck to have finally gotten the unpacking under control only to wind up with another household worth of crap in the house, but there's a lot of "why the hell did you bring all these useless old computer books, and why did you unpack them onto my one remaining bookshelf?" -- John is taking it in good humour; I want to burn all the things. Have not thrown him and his junk out of the house yet, shockingly! But he may be buying a shed to temporarily manage our stuff problem. Not kidding.

- I'm still settling back into a new routine with two of us in the house instead of just me. I like having milk mysteriously appear in the fridge!

- Work is still settling in. I am irked by the fact that I miss paperwork deadlines because I don't know about them until after they've passed, but I think I'll be able to predict some of them for next time, so I have hope I'll be able to be responsible and not on academic-time always! I've got a project on the go and will be giving a prelim talk on the subject on Thursday. I'm debating if I can find some clever way to do an off-the-wall presentation here, just for variety, but think this will be more of a led discussion.

- After much fuss, I have most of a dev environment set up again for Mailman hacking on my laptop. Looks like I probably can't justify Pycon, but am still hoping I can make the sprints. (Work may have a visitor then, though, which would mean I'm stuck here.) Either way, have a bunch of summer of code stuff that I really want to have integrated. Maybe this weekend I will actually sit down and do that. I have been a very absent dev for the past few years due to thesis, and I'm a little nervous about getting back to it, but there's lots I want to do!

- Also, I have started keeping a list of all my "I should really do this..." projects, which I find strangely motivating because so many of them seem within my grasp. I'm trying not to over-extend myself, but little personal private ideas don't feel like they're in the way. It's more like now, when I'm bored, I know I can grab something off the list.

- I totally managed a step class at altitude before I left for California for the weekend. But I also managed to make myself very sore between that and playing too many kinect games the night before. Am slightly afraid for my next class (weds unless I wimp out), but at least this time I wasn't gone long enough to lose my entire altitude adaptation. I have to say, it's a neat and unexpected perk that the university provides me with a free fitness class pass! If it turns out step doesn't work for me, i can switch to a variety of other classes, but I figured step was the most familiar class for me to start at: I know how my body should react to doing step at sea level, which gives me a handy baseline.

- That said... I managed to get a migraine for the first time since, uh, I had a root canal done many years ago which apparently fixed the freaked-out nerve. This was the day *of* said fitness class, so trigger could have been over-exertion, dehydration, altitude, or possibly plain old lack of sleep. Hopefully this will not be a thing in the future, but as far as migraines go it was kinda fun: I still have prescription drugs left over from before the migraines were cured, so it didn't hurt, and I got some seriously fascinating aura stuff happening with half of my vision flashing white shiny-ness. It made the trip to home depot especially trippy.

- I bought some "water crystal gel balls" that are absurdly fascinating given that they look like tiny plastic ball-bearings and then swell up to be marble-sized bouncy gels. Soon, I'll have some bamboo stuck in them and will have continued on my plan to green up the house (currently only at 3 plants, but I'll have a jungle yet!)

- I also bought a little nail buffer/shiner thing, which is just a bunch of different very fine grades grit used to make nails shiny without polish. This is much more fun than it has any right to be, but it encourages me to keep my nails longer than usual, which feels odd because I tend to use the tips of my fingers and thus I'm knocking them on stuff a lot. Strangely, this reminds me that I need to get back to practicing clarinet so that I'm in shape to join one of the local concert bands.

- As you can tell, I'm not actually that good at anti-materialism despite my constant complaints about the amount of stuff around here. le sigh.

So... overall, things are settling again. I'm happy to give myself a little longer of settling given that house stuff is still taking up a lot of my weekend time, but I'm hoping that I'll move past settling and into doing new stuff soon!

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Despite the the cake and cards celebrating my birthday, I don’t think the implications of being 35 really sunk in until I got on the treadmill last night to practice for the Winterman run and had to update my age. I know it’s just used for target heart rate calculations, but it was a bit of a slap in the face to know the machine’s grading me on a downward curve.

To spite the treadmill for making assumptions about how fit people my age should be, I ran a little faster and further than normal, fueled by leftover cupcakes.

I was at the hardware store again last week and needed a couple of things from their loose hardware area. Two bolts, four washers, four nuts. It was like 24 cents worth of hardware that I needed to make a pair of handy clamps.

I bring the bag to the checkout and the lady looks at the numbers I drew on the bag – 2 of xxxx, 4 of yyyy, and 4 of zzzz.

Even though I tagged the bag, I guess they make the cash people double-triple-quadruple check everything. She spent a while scrutinizing the bag from the outside, flipped it and recounted from the other side, stuck her hand in and felt around, scrutinized again… Finally she pulls everything out, lays it down on the counter, sorts them into groups, compares against the bag list again, considers for a while, and ONLY THEN, finally like forever minutes later, types it in.

Pop Quiz: Can you count to 10?

I’d have to be just about the worst, most desperate shoplifter ever to sneak a washer past a cashier -in- the bag I presented to her. They cost literally pennies and must be the cheapest single items in the store. Imagine the paperwork if they inventory their washers and come up one short!

As I was playing with them at home, I saw that there are teeny-tiny numbers printed along the edges of all the hardware – maybe she was actually trying to read every individual nut to verify? I don’t know what she gets paid per hour, but there’s probably some economic benefit to actually trusting the customers.

Incidentally, the clamps work great. If you’re ever looking for a bolt that fits your camera tripod mount, it’s a UNC 1/4-20. With a washer and a nut you can lock your camera down to just about anything.

I went back to life drawing after a bit of a hiatus and had a really good night – I even exceeded my expectations a bit and managed to not horribly embarrass myself with my final drawings. The guy posing (Jarl) was a real pro – he was doing crazy dynamic poses using a chain hanging from the ceiling, and he was super ripped so he was easy to draw. Sitting still for 20 minutes is challenging – doing the crazy stuff he was doing was pretty tough. Kudos to him!

I'm taking an online course on How to teach webcraft and programming to free-range students taught by Greg Wilson, who some of you may know. If you don't know him, you might want to listen to this talk he gave at CUSEC several years ago. Anyone who's ever thought about the world critically will probably get something out of that talk, though it was geared undergraduate software developers.

Our first assignment is to look at these recommendations about best practices to improve student learning and Greg's post about which of these he's managed to apply, then write about how we have or haven't managed to incorporate these ideas into our teaching.

( A story about pencils, 7 recommendations, and a lot of discussion... )

Conclusions?

So, lots of these things work and are common practice in my classroom experience, but not so many as far as mentoring goes. I think a few of them could apply more if I was looking for/creating opportunities for discussion and revision, but the past couple of years I haven't kept close enough tabs on my summer of code students' work to be effective at leading them down those paths. Definitely food for thought! But i feel like some of it, like quizzes, would feel incredibly forced outside of the classroom environment. Plus, repeating stuff just isn't that much fun... but maybe it could be?

Ages ago, a friend was telling me about a role-playing game she was in where she had to level up her Jedi (or maybe it was Sith?) by doing things like making web pages or doing photo editing and taking quizzes on the software she learned. I thought it was interesting that this group of people was clearly trying to help train their members outside of the game while they were training their characters in it, a gamification of life long before I'd ever heard that term (or, perhaps, before the term had been invented, though I do so love the assertion that Weight Watchers with its points is one of the most well-known examples of gamification of life). Anyhow, her game included little photoshop and story writing contests and such that seemed to keep her engaged and interested in her game "assignments" -- I wonder if there would be ways to bring some of that to free-range programmers? We have contests, but not at learner levels. We sort of have ranks as open source developers sometimes (bugs solved, commit access, invited to maintain $foo), but they're often not explicitly defined so it's hard to use them as motivation.

This might be interesting, but I can't shake the feeling that trying to force things like quizzes to work for free-range learners might be like clinging to the pencil as a way of learning.

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Yesterday was kindof a disaster for buses – we were getting sleet and freezing rain, so inevitably they were running really late and/or were too full to pick us up when they came. Finally a 176 stopped for a gang of us on Merivale, and we packed in like sardines, only two blocks later to get rear-ended by a car (who drove off). Official bus policy is that everyone has to get off and wait for the next bus.

Forget that – I’d already been outside for an hour and a half and I couldn’t stand around anymore. I decided to walk. It wasn’t that bad, really, except that I had a bag full of dinner and was looking forward to getting home. I was facing away from the rain the entire way, it was pretty warm out and I’d dressed properly. But my coat was getting stiffer as I walked – when I get home I saw why. My coat and bag had literally frozen solid all along the backside.

I read a while back about Reaction-Diffusion algorithms and always wanted to try them – really neat organic patterns (like leopard spots and fish stripes) can be modeled using a surprisingly simple set of rules. This works kindof like the “game of life” algorithm – you throw down a bunch of noise, and the pixels move around following simple rules (they basically “diffuse” outwards). But in this algorithm, each cell also produces an inhibitor, which forces the pixels to clump up, producing all kinds of neat-o organic patterns.

It’s a really elegant algorithm that in a simple way mirrors what’s happening with things like pigmentation and growth formation in living systems – I thought this particular set of rules looked kindof like brain coral. It’s fun to look for patterns in the shapes – it’s like looking at clouds, except after a while your eyes hurt!

(Brain Coral from the USGS Archive)

The scare quotes are because neither of these things should have been accomplishments at all, since they should have just worked. Since they didn't, though, I'm blogging for posterity with links to the things that helped me solve the problems.

( Short version: I now have 8gb of ram that works, a backup drive that doesn't, a Mailman dev environment that half works, and I kinda hate Apple. )

I'm tired and cranky, but I'm determined to win this... tomorrow.

Also, I made myself cookies, so that's something.

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I was talking in an earlier post about my slide photography rig – I’ve been messing with different techniques for capturing the slides since then and coming up with some ideas. I had an interesting brainstorm on the weekend which turned into a failure for unexpected reasons, and I thought I’d share.

After rummaging through the basement and a trip out to the hardware store, I managed to build a rudimentary fluorescent lightbox that works pretty well (successes are boring – more about that later). After all that effort, I suddenly realized what an idiot I’d been: I had been staring all along at readily available lightboxes all over my house – backlit lcd monitors!

It suddenly seemed almost too easy: Open up a blank white document, sit the slide on the bevel of my laptop screen, and snap a digital picture!

But something unexpected happened – the slide is so small that when I got a macro shot of the picture, I could see the pixels of my lcd! They’re not visible to the naked eye, but when you’re stretching an inch of film out to 3000 pixels wide, and doing a relatively long exposure through a piece of opaque film, the brightness difference between the pixels and the troughs becomes really vivid.

So it wasn’t so stupid of me to build my own lightbox after all! There’s a couple of easy ways to get around the pixels showing up if I was really dedicated to using a laptop screen as my light source:

1) Put a diffusing material, like some white plexiglass, over the screen. I’m basically doing this with my “real” lightbox already. This should smooth out the pixels underneath into a uniformly white area.

2) Easier: Bring the slide forward off the screen and shoot with a wide open lens so the pixels blur in the background depth of field

3) Harder: Open up the monitor, peel all the LCD layers off and just shoot slides against the solid self-illuminated background layer. (If I had a broken LCD kicking around someplace I might consider this)

Once upon a time, there was a blog aggregator for Women in Free Software. Then it broke. Repeatedly.

I found I sort of missed the FOSS Women Planet, so I made myself a new one: http://terri.zone12.com/wifs/

That's currently seeded with the feeds from the original list. I know lots and lots of women who aren't on the original list but who do have public blog feeds, so I may add some from my own reading lists. Meanwhile, if you'd like to be on there, feel free to let me know, and if you also missed the old one, feel free to use mine.

I'm thinking maybe I should get a better url for it and make this more obviously a public thing that others might read, but I don't currently own a suitable domain. Suggestions? It's tempting to make womeninfreesoftware.nowwemustfight.com but I'm pretty sure that's not the impression I want to give.

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