Sunday, August 20, 2006

week of work

This last week was pretty uneventful. I worked. There was a DAS sprint last week and while I wasn't in California for it I did participate from here. It started in the evening with a 6pm phone conference call. For the first few days I went to a cyber cafe nearby. I figured I would talk and use their bandwidth instead of the DSL here. There's usually a 3GB/month cap and I have no idea how much of it I've used. I've been putting off downloading movies and large images, cvs updates, things like that. The noise was too loud though, being on Main street. For the last couple of days I did the call from here. Last January when I did a conference call I used a phone card but there's no land line in this apartment so VOIP for me.

For the sprint I updated the spec and implemented a reference server. I've used the latter as a practice piece for learning more about TurboGears, SQLObject, SQLAlchemy, and other bits of techonology. I understand a bit better why people have raved about SQLAlchemy. There's a few bits I'm still shaky about.

Usually I would work on the sprint until about 3 or 4 am, with breaks. I'm usually a go-to-bed 2am person. I've found that without an alarm I sleep about 8 hours. Waking up at noon seems like a waste of the day. When I've pushed my schedule that late I end up being groggy for the first few hours. And then it's time for another phone call.

The last day's (evening's) call was the strangest. Everyone else (US sprint; the UK people didn't participate in this one) wants a change to the basic feature data structure. It's strange because it makes no sense to me while to everyone else it's obvious. I'm the spec author so I'm the one that needs to be convinced. I also need to resolve this. My approach Friday evening (after the call) was to figure out a difference between the two.

I'm a protein guy by training. The examples bought up in the conference call to justify the reasonableness of the change were all DNA oriented. (The short version is: if a child feature has a location then the parent feature must have a single location on that segment and it must cover all the locations in the children.) My counter examples were all protein so I worked some trying to find DNA-based counter examples. I came up with a couple, but I know so little about DNA. I have to stretch back to '93 when I learned some of the basics of regulatory factors.

I think the reason for the difference in viewpoint is because DNA as a physical thing is very boring. And I say that with the highest respect; proteins get all the action while DNA mostly sits there. Only a small bit of the human genome even gets transcribed. Some into protein, hence the annotations are pretty indirect. Some proteins bind to DNA to promot or inhibit expression of certain genes so these are a bit exciting, but the binding sites are all small, contiguous regions. BLAST results have gaps but the region in the gaps is relevant so even there having a single covering location for the parent makes sense.

Compare that to a protein annotation like "catalytic triad" where a location for the parent element for the three features (assuming a feature per residue) makes no sense. Digging around I did find some annotation types where having a parent with a single location covering all of its children didn't make sense: D-loop in mitochondria, promotor groups (multiple promotor sites for a given gene), and RNA/ssDNA structure and catalytic function.

Today I tried another approach. Assuming the data structure is changed what are the consequences to the spec and does the result make sense. My conjecture is it's needed to make the "inside" search work correctly, but I think the solution doesn't interact well with the other query types. I also think the "inside" search isn't needed and a better solution to the use-case is a "but_not_overlaps". We'll work this out over the next couple of weeks.

Saturday afternoon I went to the salsa clinic. That's the monthly event at Que Pasa where John reviews the previous month's lessons over 90 minutes. I learned a few nice additions but if I don't practice them I'll forget them. Towards the end I danced some with .. I don't remember her name. She was quite good and fun to dance with. QP has more space than Buena Vista which means I can do things which take up space. At BV I often feel constrained in what I can do because it's so packed.

James and Amanda's house^H^H^H^H^Hflat warming party was last Friday evening. I snuck out for a few hours for that. I brought a couple of cans of Swedish cider as house warming gifts, which they enjoyed. Cider here is like British cider; dry and a bit. Bit. I don't know the right word. "flat", "muddy", "wooden" come mind. So does "slightly sour." Swedish cider is sweet and carbonated. Jim (Cooper) called it R-rated Kool-Aid.

Saturday, August 12, 2006

Two Oceans Aquarium

I forgot to mention that handshakes are different here. Depending on who you meet it's the standard clasp, a quick triple from standard to inverted (like when arm wrestling) back to standard, or a triple plus a snap at the end. I like the triple but I can't get the snap down.

I asked one of the guys at salsa about kissing customs and his answer was "no one knows." Helpful.

Today I went with Nicole (not SANBI Nicki - must get ahold of her too) to the Two Oceans Aquarium. I was a few minutes late as I didn't plan on enough time for getting gas and money. Gas here is expensive. Filling the little car took 200 bucks or USD 30. It really can be called bucks here because there's a springbok on the 1 rand coin. Still, $30 isn't much more than in the US now, and much less than the UK or Sweden. Gas stations are all full service so I rushed in to the ATM to get money while the guy filled up the car and washed the windows.

It's a decent aquarium. The "Two Oceans" name refers to the South Atlantic and Indian Oceans. That's cold kelp waters and warm tropical, making for some diversity. My three favorite individual species were the seals, the penguins, and the deep sea spider crabs. Seals and otters always look and act so happy. The penguins acted more like dog in how they paddle when the head is out of the water and one in how it scratched it's belly. The spider crabs were just cool. I wasn't so much interested in the other crabs and lobsters through, except to see more of the dynamics of an exoskeleton close up. I had read something about that recently poining out how the legs are joined via a sort of pin snap.

The layout was similar to the Monterey Bay Aquarium in that there's a natural path through the site which takes you by everything without backtracking. Unlike the World of Birds where it's easy to get lost. (They have more exhibits and each is smaller so the dynamics are different.) Also like MB you see the big aquarium and go "oooh", watching the fish for a while. In this case it was the kelp forest. After that is the really big aquarium, with the sharks and rays and other big fish. (In MB you then go to the "someone misplaced an ocean" sized aquarium. With the half-ton tuna fish. But no fair comparing TO to one of the top aquariums in the world.)

I've decided I don't like starfish. Something about them gives me the shivers. Probably stories about how they destroy sea beds, attacking and eating anything.

Wednesday, August 09, 2006

pirates and kissing

I went to Pirates of the Caribbean, Dead Man's Chest today. Only R20 = US$3 for the 6:15 showing. That's what, a liter of gas or so? I don't actually know the price because none of the stations list the price of fuel. I imagine it's visible on the machines but every place is full service so I've never looked. I could check my receipt but that would mean rooting around for it and the last time I may have just paid, said "keep the change" and left without getting a receipt.

I met James&Amanda there and two of their friends. I thought it was an amusing diversion. I enjoyed the Davy Jones character. The movie had the feel of 1950s B movie filtered through the memories that make the things of youth so much better than the present. "The 3D graphics in Zaxxon were so realistic." The movie had elements from Zorro, 20000 Leagues under the Sea, and even a bit of Apocalypse Now. J&A didn't like it. It did make me feel like watching a movie by Salieri, technically well done but without the something extra Mozart would do. Assuming Amadeus had any reflection of reality. Amanda especially didn't like the sound quality in the theater.

Afterwards I went to tango. PotC2, btw, is a long film. If this is Tuesday then I must have gone to Rouge. It was a decent night but nothing really grabbed me about the music or dancing as it can on the best nights. At the end I said goodbye to one of the women and got a kiss.

I need to explain that. This is a kissing culture. Often on hellos and goodbyes there's a single kiss on the right cheek. Sometimes also on the left but that's rare. I still haven't figured out the full dynamics of it: is it a direct kiss (lips flat on surface) or an angled one? (More the latter. The one guy I know who does the full flat kiss does it in such a way that it's obvious he's doing it in part for show.) Does a "oops I forgot about the kiss and ended up with an air-kiss" count as a faux pas? Probably not.

Kissing on the cheek is not unusual. There's even a FAQ somewhere on how to do it, with comments about the different styles in different places. (left and right cheeks, or L&R&L for some cases). What I've not seen elsewhere is kissing on the lips. Chastely, just like kissing on the cheek is a friendly gesture and no more. It happened once with salsa and tonight it happened with tango. The contexts were different though: in salsa it was someone I danced with several times before, we dance well together in general, and we had just finished off a great set. While here it was someone I've danced with on two nights and that's it.

Niven in his Known Space stories postulated that the STL-spread human colonies would diverge enough that unrealized non-verbal communication could accidentally break a relationship. That's no great stretch of a prediction. There was an ad years back for some international business consulting company. It showed a western backpacker in southeast asia. He relaxes and puts his feet up on a chair. Various people laugh and look at him funny. Showing the bottoms of the feet was considered rude there, explained the voiceover. That's why when you enter the world market you should hire them and their international experience.

After my last visit here I brought some of the cheek kissing tradition back to Santa Fe. It's a different context, different milleau and I would only do it with a few people I knew well from dance. It didn't catch on. I wasn't surprised.

Monday, August 07, 2006

Fresney and Glencairn

It looks like this is, or more likely the tail end of was, the Jewish section of town. There's a building a couple blocks from here with "Shalom" in the entranceway, the local office copy place will make invitations for a bar or bat mitzvah and the grocery stores have decent kosher sections. One has a sign saying "Ferrero Rocher Chocolates are kosher". Oh, and they stock pastrami and rye, though I think that's more a stereotype these days than being a strong indicator. I like p&rye. In Cape Town there are many restaurants which include mention on the sign that they are serve halal foods. I don't think I saw any places here with a similar mark for keeping kosher. I was in a scout troop growing up. The meetings were at Temple Judea in Coral Gables and some of the scouts were Jewish, but Reform Jewish like most on the US. Two of the scouts (Matt and Matthew) celebrated their bar mitzvah together and Matt invited me. Men and women sat together and I was not asked to wear a yarmulke. There was only one campout I can remember where we needed to keep kosher. As the meal was spaghetti it was mostly a matter of keeping the dishes and utensils separate.

Yesterday I went to Glencairn to visit Mariana and her husband. I think it's actually Glancairn Heights in the way that my grandparents lived in Sebastian Heights, where Sebastian was little more than a spot on the map. Their house is to the east of the 4-way intersection in the middle of,18.431432&spn=0.002548,0.003428&t=k&om=1 . Zoom back and Glencairn is on the south side of the valley. Rather smaller than Sebastian.

Zoom back some more and look a bit south. That's Simon's Town. The jackass penguin flock is near there at Boulders Beach. Yes, one of the three current penguin colonies in South Africa. Simon's town is the base for two of South Africa's naval vessels. Both are moored in Google's satellite image. Look southwest, up the hill and due north of the small dirt airstrip is a radar installation. It used to be (and perhaps still is?) a law preventing people from taking photos of this area of South Africa. In 1982 the base commander, Dieter Gerhardt, and his wife were arrested and convicted of being Soviet spies.

There's a train which runs from downtown Cape Town all the way to Simon's Town, hugging the coast from Muizenberg on down. Where's Muizenberg? Follow the coastline up until you get to the wide sandy beach. That section in to the city is known as the Cape Flats. This peninsula is known as Cape Peninsula and is the east side of False Bay, so named because sailors coming from the east would confuse Cape Point (at the end of the peninsula) with Cape Hangklip (at the end of the Cape of Good Hope on the other side of the Bay) and think they were coming in to Table Bay.

People have said the train trip down is scenic. I can believe it, at least for the last bit. Especially if the whales are in the bay. Mariana said she say a Southern Right whale a few days ago, but none came by for a visit that Saturday. Cape Town does have mass transit. There are several train lines and various busses and minibusses. There's even a bus stop across the street from where I am but it does not come frequently. Cape Town's core is pretty compact, being from the pre-car era. It's sprawled since then and cars are the only way to get around unless you want to wait a long time or don't have money. Which is true for a lot of people.

One reason people don't take train even when it goes the right places at the right times is a nervous worry about crime. Everyone locks their doors, and often with multiple layers of locks. There are three between me and the outside - apartment door, complex door, and security door outside that, and the complex walls are topped with razorwire and electric fence. There's a fear - justifiable? - that taking mass transit is too much of a risk. Growing up in Miami I recall taking the bus once, in Cub Scouts to get back from the zoo. I had heard that a lot of strange people took the bus, but not that it was unsafe. My faint memory was of someone in the bus was curious about us - the pack of boys was the strange event.

The next World's Cup is scheduled for Cape Town. A big worry is, will there be enough infrastructure in place to host the event? There's talk of building new stadiums and improving the rail system to handle the .. hundreds of thousands? .. of fans expected to come. (If US college football teams can bring in 40,000 fans+ then world cup soccer can surely bring in more. And it's "soccer" in South Africa and not "football" like it is in the UK.)

Another facet to this story is that some of South Africa's infrastructure has gotten worse since the fall of apartheid because of switching funding to improve social services like, oh, education and health. There's an interesting tradeoff which I'll simplify thusly: should we spend less on the power grid so blackouts become more frequent and spend the money in education so the next generation will have better careers and be able to pay for and do the needed improvements? By how much? How long wlll it take?

In Sweden 4 of the country's 10 nuclear reactors were shut down lat week because of safety concerns about backup procedures. I think 2 of 4 backup generators failed at a plant when there was an electrical outage. While 50% of Sweden's power comes from nuclear plants, taking 20% of the production off-line didn't cause black-outs, only more expensive power. You can do that when you have money and planning. Lat summer here (February) one of the Cape Town generators was off-line with a hard-to-replace part and there were rolling backouts for several weeks. Then again in the US this summer (now) I'll guess there aren't many parts of the country which can take a 10-15% power loss. Everyone loves a/c. Though not my dad when growing up. We were one of the few places in Miami with no a/c. Lots of fans and windows but no a/c. We didn't have heat either but that's less of a surprise. Most modern houses are designed for a/c and are nasty hot and stuffy if you don't have it running in hot weather.

Here it's winter. I wouldn't mind trading a bit of that heat for some of the chill of my bedroom. Or mind using a sauna or hot tub.

Thursday, August 03, 2006


It's raining cats and dogs here. There are poodles everywhere. Including the one left my my upstairs neighbor's dog. The rain should give a good soak to the ground for the wine. I was here last year so knew to expect the cool wet days of winter. I rather like it. Perhaps after 8 years in the high desert I like seeing grey mists. My favorite season in Santa Fe was spring, when the clouds drop down into the mountains, young and gentle and not yet the anvil heads of summer.

I just came back from Que Pasa, a salsa bar downtown. John runs the place and teaches lessons on Tuesday, Thursday and Saturdays. His style is different enough from mine that he does things that I've never done, which is fun. The intermediate class today was a two hand connected right pass into a back-to-back copa. I've done that before. But afterwards he went into a reverse hammerlock then a double turn into a regular one then a cross-body for her followed by a paddle turn for him with left hand connected coming back into closed position. Got it?

That was neat. Then there was the advanced course, which was based on Tuesday's lesson. I went to tango instead. So I had to catch up. This was much harder because there were several moves I've never done before. First a right pass in closed position (I've forgotten the name though). Continue into a cross body lead with left hand on shoulder. The new part was this quick 180 turn with the lead and follow essentially going in a circle swapping positions (he walking in a curve backwards while she's forward). It isn't LA/line style but it is John style. From there the lead does a full right turn swapping hands to handshake position. Lead her into a broken left (via a start into underarm turn then check her into reverse; I just figured out now that we were doing a broken left). Take her into a cross body while he comes around in reverse (to the right instead of following her). Then do this spin thing with her arm - I don't know the name of it - to step facing away from the line and lead her into an cross body lead inside turn. Stop her when she's done one turn (so in sweet-heart). Then do a turning 1-2 so she's facing forward on the line into a cross body double inside turn finishing with a spot turn for him back to two hand open position.

I barely got it by the end and should practice it some more. One problem was there were only 7 women and 11 men in the class so we had to stand out often.

I enjoy the Cape Town dancing. I think I've written this before but I'll do it again. The Sweden and UK salsa dancers are technically better than the people here, but I have so much fun in Cape Town. There is something to the stereotype of most Scandinavian people being reserved while here it's more .. playful? Flirty is probably the best word, though I don't think of myself as a flirt. Looking it up I see the ambiguity in the term: one place uses "playful behavior intended to arouse sexual interest" while another says "talk or behave amorously, without serious intentions" while wikipedia says "casual conversation with a romantic touch, but it need not be spoken interaction". The last feels like the best fit.

In Cape Town

I'm in Cape Town now. IKapa in Xhosa (the leading 'i' indicates a noun - iColgate is toothpaste.) I got here about 2.5 weeks ago. The first two weeks were quite demanding as I was teaching from about 9-5 each day and preparing for the next day in the evening. On top of that my house sold last Wednesday and there were the final back-and-forths. Turned out the roof and electrical work weren't in good enough shape for the buyer's inspector. I went along with the contractors' estimates and escrowed about $10K for repair work. All that kept me busy and not only did I not get time to write I didn't even go out dancing.

I started again last Saturday evening: tango at La Scala in Cavendish mall. It was nice to see people I knew from previous visits. One of the advantages of Cape Town over Göteborg is language. Most of the conversations were in English, helping me feel like I was part of what was going on.

As I think I wrote earlier I decided I did break my right foot's 4th toe while at tango camp. Saturday was the first time I wore my latin heels, which puts more weight in the toes. I was pretty ginger in dancing and felt rusty. They dance differently here than in Gbg or Santa Fe (regional accents) so most of the dancing was more like calibration as I would not infrequently lead something not often done here, or in a different manner.

Sunday I went salsa dancing at Buena Vista Social Cafe. I've joked about how weird it is to go to a Cuban place and see pictures of Castro, Ché, etc. Growing up in Miami, with a father and grandparents who lived in Cuba for several years before the revolution, I think I have some idea of what Cuba is like. But Miami culture, more in the older generation, is very anti-Castro and is a branch from what Cuban culture was like in the mid 1950s. Some years back in Santa Fe I went by the Cuban restaurant there. The lunch menu included sandwiches, including "The Castro". In Miami post-Mariel I remember (or misremember) that a local radio commentator's car was fire bombed not because he was pro-Castro but because he wasn't anti-Castro enough. I can't imagine a Cuban place in Miami ever selling a sandwich with his name.

Again it was great to see familiar faces from last time and have women come up to me and hug me and welcome me back. Cape Town is a more demonstrative place than Gbg. I got caught up a bit with what's going on in the local salsa scene, and got to show off some of my foreign dance accent. Best was dancing with Lenine again - we've got a great connection when dancing which brings out something extra in me.

On Saturday I started looking for a place to stay while in the Mother City. I hit various Cape Town vacation rental sites looking for an apartment available for a month with broadband and within 10 minutes of city center, available for a month and under R300/day. The hardest of these was the DSL connection. But I managed to find one. Here it is:,18.384542&spn=0.002555,0.003428&t=k&om=1 . It's the apartment building in the middle with the light blue roof, on the corner. I'm on the corner next to the largish road, Kloof St. i haven't met the owner as she's out of town - in Norway.

I moved in Monday day. That evening I went to tango class as El Cacha. Tuesday was the weekly tango event at a restaurant in Cape Quarter, which I think is in the center of,18.384542&spn=0.002555,0.003428&t=k&om=1 . If not, it's in the same image. I was there at night making it hard to know what's where.

There too I started feeling rusty. As the evening progressed I got more back into tango. (Hmmm. That last sentence isn't correct English but it works. What about "I regained more of the sense and feeling of tango"?) I had some excellent dances, wth the caution that there wasn't enough space. The restaurant didn't have much floor space so some things I couldn't do.

Tonight was a bummer. I misread the time for the milonga class as 9:30 instead of 8 pm. It read "3 August 8 - 9:30" and I think what happened is I read it as "August 8th, 9:30pm" because US dates are "month day" and not "day month" like it is in most of the rest of the world. I thought 9:30 felt late but I knew that normally there's a practica from 9-11pm nd figured it replaced the practica time slot. Nope. Sadness.