Wednesday, June 29, 2005

Craig Venter goes synthetic

Synthetic biology is becoming "real", at least in the sense that actual companies are being founded based on its promise. The first one I heard of was Codon Devices, which has a pretty heavy-hitting board of scientific advisors, consisting of almost all the high-profile names in the field. The second entry into the fray is Craig Venter's latest venture, Synthetic Genomics, which hit the media today with a press release and even got a write-up in the WSJ.

I still think the overall synthetic biology concept is really cool and haven't totally given up on possibly doing something in that area as part of my thesis, despite not joining Drew Endy's lab -- RNA [which my lab specializes in] has already been used in a couple of synthetic bio papers as a way to control gene expression [check out this review if you're interested].

Tuesday, June 28, 2005

These are not the stem cells you are looking for

MSNBC has an interview with one of the pioneers of embryonic stem cell research, in which he makes some thought-provoking claims that the major contributions of stem cells to human health probably won't be what most people think they will be. Interesting reading.

Monday, June 27, 2005

Wandering in the microRNA wilderness

Pretty much my biggest goal for this summer is to find myself a thesis project that involves working on microRNAs. I feel a bit like Goldilocks in that I want something that doesn't have too much wet bench work, or too much computation, but is just the right mixture of the two. Oh, and I'm picky about what kind of computation I want to do too -- I want to do something "systems-y", something that is related to the dynamic behavior of a system, which means I don't want to do any/very little sequence analysis. And it'd be nice to work with mammalian cell types in which microRNAs have been shown to play a big role, like blood stem cells or embryonic stem cells.

To get some ideas for thesis topics, I've been reading the existing microRNA literature, in a somewhat scattershot fashion. The papers out there seem to fall into a fairly small number of categories [the links are to pseudo-randomly selected papers in each genre]:

1. Computational prediction of microRNA genes and microRNA target genes, with a bit of experimental validation tacked on. Everybody and their mother seems to be working on this, with a couple of papers published [almost] every week, trying to outdo each other in terms of how many microRNAs and targets they predict. The modus operandi seems to be "more is better".
2. Hard-core biochemistry aimed at trying to figure out the actual molecular machinery of the microRNA pathway, like so.
3. Papers of the form "microRNA X affects process Y because if we take away microRNA X, process Y breaks down", like this.
4. Studies along the lines of "This is what it looks like when you track microRNA expression levels during the development of organism Y [but we don't really have an explanation for the changes in expression level]", for model organisms like zebrafish.

... and then there are a bunch of review papers that try to make sense of the flood of data.

Now, these are all perfectly reasonable things to do, but none of them really float my boat -- type 1: sequence analysis, blergh; types 2 & 3: no computation involved; type 4: so far, the only type of computation I've seen in this sort of paper is some pretty mundane clustering.

In other words, systems biology-type work on microRNAs seems to be non-existent at the moment, or [more likely] not published yet. I think that's because the microRNA field is still relatively young -- to build a detailed differential equation-based/stochastic model of a particular genetic pathway that involves microRNAs, you need to know what turns microRNA expression on/off and what the targets of the microRNA are, and the majority that knowledge simply doesn't exist yet. The other systems bio approach, namely taking a bunch of expression data and then trying to reverse-engineer a network out of that [eg via Bayesian networks] relies on having a reasonable amount of decent-quality expression data, and that doesn't exist yet either [partially because there's still lots of debate about what is and isn't a microRNA, and the list of known microRNAs keeps growing]. Throw in the fact that the microRNA pathway only exists in metazoans [ie multi-cellular animals], and those are much more complex and less well-understood than the bacterial/viral/single-celled eukaryotic organisms that most systems bio work has been done on so far, and it's not surprising that there's a dearth of that kind of research.

From one perspective, this is good news -- it means the field is wide open, unlike the pig pile that prediction of microRNA genes and microRNA targets has become. From a different perspective, it's a bit frustrating to not have any obvious "prior art" from which to draw inspiration [or maybe I just don't see it yet].

In the meantime, I'm just going to keep thinking about things I could do and hope that inspiration strikes sometime soon. Oh, and if you have any ideas that you can bear to part with, feel free to send them my way ;-)

"The endurance is strong with this one"

My boy Brandon is officially a Man of Iron -- yesterday, he finished the Coeur d'Alene Ironman, in his first-ever attempt at a full Ironman. Along the way, he racked up some pretty impressive training stats. Having endured that volume of insane training myself for various taekwondo competitions [a stage I am thankfully past ;-)], I can truly appreciate how much mental and physical effort went into it, especially given that he was training alone. At some point, the mental part becomes as hard as, if not harder, than the physical bit -- persuading yourself to roll out of your warm bed at an ungodly hour so you can inflict pain on yourself for the next few hours, for months on end, in sickness and in health, regardless of how much sleep you got, requires a serious commitment, even more so when there's nobody sharing the pain with you. The "why are you doing this ?" question gets louder and louder; at certain points, the best way of dealing with that question is to ignore it and focus on your workout. Obviously not a good long-term strategy, but it'll help get you through the rough spots.

In any case, congratulations, B ! You are The (Iron) Man !

Weakest comeback ever

Exhibited by GW in response to a question about the Iraqi insurgency supposedly weakening, starting around minute 3:13 of the "Best Leak Ever" video here. And he says it like he wants extra credit for that. [Cue voice-over from the Chris Rock "N***as always want credit for some sh!t they're supposed to do; you're not supposed to go to jail, you low-expectation-having motherf!ckers" skit ...]

The optimist in me says that, surely, we must have reached at least a local minimum in the "Worthy-to-be-president" energy landscape, so the next one has to be better [assuming that we're not jumping around randomly in the landscape]; the pessimist in me mutters "Yeah, but if this is just a local minimum, think what the global minimum is going to be ...".

Saturday, June 25, 2005

Hey, did you order a pizza ?

Steven Colbert, of The Daily Show, does an interview with Mary Carey [follow the link and click the "Popping a big tent" link], the porn star [and former gubernatorial candidate for California] who recently attended a Republican fundraising dinner. In the interview, she presents some very good reasons for becoming a Republican while also exhibiting other charming, uhm, eccentricities. Highly, highly recommended if you want to laugh your @$$ off.

[Yes, yes, I know, it's the liberal media putting an anti-Republican spin on the whole thing. She's actually hiding a razor-sharp intellect behind her permanently-attached flotation devices.]

New and used disk worldsheet instantons, only $6.99 !

After initially following a link off BioCurious and then getting sucked deeper and deeper into the vortex, I think that theoretical physicists are either playing a huge practical joke on everybody by pretending to say things that make sense but really don't, or you should be able to buy your very own warp drive for only 5 low monthly payments of $19.99 in about 6 months.

Consider this little excerpt from the blog of a theoretical physicist, talking about string theory:

It is also conceivable that someone - or a group of people - is very close to identifying the correct background of string theory that describes reality, and it is a matter of weeks, months, or years before convincing evidence that their background is the correct one will emerge. Among the promising backgrounds, I would list:
  • the weakly coupled or strongly coupled (Hořava-Witten) heterotic strings with an "E8 x E8" gauge group and an appropriate Calabi-Yau - the most interesting recent example is the Heterotic Standard Model. This is the class of models that gives the most natural explanation of the particle spectrum - namely the fermions being naturally grouped into grand unified families.
  • asymmetric orbifolds and free fermionic heterotic models - it is related to the previous item but the Calabi-Yau is replaced by fermionic worldsheet degrees of freedom that are roughly equivalent to a Calabi-Yau near a self-dual radius. While many advantages of the geometric Calabi-Yau backgrounds are preserved, a natural explanation of the number of families (three) may be given in the free fermionic models.
  • intersecting brane worlds - type IIA with orientifold planes and D6-branes and matter that lives at the intersections. The most attractive feature of these models, as far as I can say, is that the Yukawa couplings may be naturally hierarchical because they arise from disk worldsheet instantons where the disk is actually a triangle stretched between the three relevant brane intersections
"Disk worldsheet instantons" ? Wha' happen ? Biology is full of jargon but at least you can get to a decent understanding of a large portion of it by doing a bit of background reading, but to understand this stuff I suspect you're looking at an investment of many years, mainly spent on really complicated math. No wonder that sometimes utter gibberish gets published.

There is, of course, also the possibility that all this makes sense [to somebody], but isn't getting us any closer to the warp drive.

Friday, June 24, 2005

Genetic cache miss

A while ago, I wrote about the mystifying discovery that a particular type of plant seems to keep a "backup" copy of its DNA around, to serve as a "genetic cache". In conversation today with one of the post-docs in my lab, who works on plants and knows a lot about them, this paper came up and his reaction was "Ah, that's all a bunch of nonsense. There's no such thing." Apparently the consensus in the plant biology community is that the results reported in the paper are due to contamination from pollen ie the supposedly missing DNA was reintroduced through pollen from another plant that was still floating around in the jars in which the plants were grown. Guess we'll have to wait and see -- if this is real, it'll reappear, otherwise it'll just quietly migrate into the "Stuff that sounded really cool, but turned out not to be true" pile [like this].

Thursday, June 23, 2005

NYT does microRNAs

[As brought to my attention by QoW] The NYT has a nice little article on microRNAs, the main focus of the lab I'm in. My advisor, Dave Bartel, is quoted a bunch of times. The field of microRNAs is pretty hot at the moment [there are new articles published on it every week, in a bunch of journals], which [I think] is a reflection of the fact that it's still relatively new and not very well-understood, so there's lots of low-hanging fruit to be harvested ie relatively simple experiments that help to illuminate the basic mechanisms of how microRNAs work. It's also a big deal because a huge number of human genes appear to be regulated by microRNAs and microRNAs participate in some pretty important processes -- blood cell differentiation, heart muscle cell differentiation, stem cell division [at least in fruit flies] etc. Understandably, the discovery of an entirely new mechanism of widespread gene regulation has lots of people pretty excited, leading to the current feeding frenzy.

Hopefully I'll get to participate in the publishing frenzy too sometime soon =)

Honeymoon: Matapalo, Where The Wild Things Are

[Previously: Malpais proves to be rather unappealing so we decide to go to Matapalo and have just made it as back to San Jose, to a hotel that falsely advertised the availability of hot water]

Once we'd accepted that there was no hot water to be had and had taken yet another cold shower, we tried to get some sleep. This was when we found out that sometimes, what you don't advertise is as important as what you do advertise. In this case, what hadn't been clear was the fact that our hotel was directly next to the main street through town and that our room specifically actually jutted out over the road. This particular arrangement meant that we got to enjoy the full auditory range of the noise produced by internal combustion engines, from trucks, cars, scooters etc. I think at one point there was even a small plane that rolled by underneath our room. All in all, not exactly a peak sleeping experience.

We got up at the crack of dawn the next morning [which was pretty easy, since we didn't really sleep anyway] and prepared to head for the airport to catch our flight to Puerto Jimenez. There was only one small task that we had to perform beforehand, namely dropping off our rental car. The instructions said to drop it off at the "airport rental car return office", so off we went to the [international] airport. When we got to the bit of the airport that had rental car offices, there was nobody around, which wasn't entirely surprising, given that it was around 6:30 am, but still rather inconvenient for us. After banging on a few doors, somebody finally showed up, listened to my explanation and then said, as if it was perfectly obvious, "Oh, you want the airport rental car return office ? That's not actually at the airport, that's back in town".

Riiiight. While sorely tempted to get into an argument along the lines of "Then why the #$@@$^^% is it called the 'airport' rental car return office ?", I merely sighed and asked for directions to the office. This revealed another feature of Costa Rican life that I guess I should have expected, given that it's the same in Ghana -- road signs and marked exits [off freeways] are few and far between, so the general gist of directions is something like "Go until you pass under a bridge and see RandomCorp on your right, then take the 2nd ... or 3rd ... exit after that, take a left at the blue billboard etc". Those sorts of directions will get you lots of things, but they won't get you to the right place quickly, especially if you're in a totally foreign city. We spent a good 20-30 minutes trying to find the office, based on the directions, trying out ever-new variations of what he might have meant, like "Did he mean the 3rd exit after RandomCorp or after the bridge ? Did you notice a slight hesitation in his voice when he said 3rd ? Do you think he meant the 4th exit ?". Finally, mostly by sheer luck and adopting a random search strategy, we happened to find what we were looking for.

At this point, we still had to get to another airport in time for our 8:30 am flight, so we rushed in, threw the keys on the counter and signed every piece of paper they shoved at us as quickly as possible. Our car had also acquired a large dent, source totally unknown, and I didn't even bother trying to establish whether that was covered under the insurance I'd paid when we rented the car -- I just took the rental agent outside, showed him the dent, said "Look, there's a dent, deal with it". With that all taken care of, we hopped into a taxi and took off for the airport to catch our flight to Puerto Jimenez.

Puerto Jimenez doesn't have so much an airport as it has a single landing strip hacked out in the middle of town. The landing strip is paved [poorly], but that's about it. This means that the range of aircraft it can accomodate is pretty limited, so all the flights into and out of Puerto Jimenez are little puddle-jumpers [the first time we went, we were in a plane that held 5 people, including the pilot ...]. The net result of this is that they have pretty low limits on luggage and charge you a silly amount for having more than their maximum. We'd totally neglected to take this into account, so we were rather unpleasantly surprised when, during "checkin" [which amounted to walking up to a rickety little table with a bathroom scale on it], we were cheerfully told "Ok, that'll be an extra X dollars for your baggage. In cash." There was no arguing about it -- our choices were to leave our luggage behind or pay up. Luckily, I happened to have enough cash with me to pay for it, barely. After that, our hour-long flight to Puerto Jimenez was uneventful.

At this point, I must digress a bit to give you, gentle reader, an idea about Puerto Jimenez, and Matapalo, our eventual destination. They are both on the Osa Peninsula, on the Pacific side of Costa Rica. Puerto Jimenez is a quiet little town that is mainly used as a jumping-off point for people heading into the Corcovado National Park, which is a huge expanse of virgin rain forest. Matapalo can't even be called a village -- it's basically a collection of houses hacked out of the jungle by really, really determined people, many of them expats. All the electricity comes from solar power, their water comes from a spring somewhere up in the jungle [which they found and tapped themselves], communication occurs via CB radio [everybody has their own frequency, so to get in touch with somebody you tune to their frequency and yell their name into the walkie-talkie until somebody answers ...] and to get there from Puerto Jimenez you have to ride in a pickup truck that is capable of navigating the totally unpaved road [which can be especially tricky in the rainy season]. To get back into town, you have to radio into town and request that a truck come out and get you, so you have to plan a couple of hours in advance. The houses are literally in the middle of the jungle, and surrounded by insane amounts of wildlife -- you're woken up at 5 am by howler monkeys doing their thing 50 yards away [a truly scary thing the first time you hear them], scarlet macaws fly by regularly, coatimundis hang out around the house, you can see the occasional sloth hanging from a tree, huge blue morpho butterflies flutter around ... you get the picture. Put all this together with pristine beaches, warm water, several surf breaks and you truly have an unspoiled tropical paradise.

One slightly dark side of this bit of paradise, at least from a surfer's perspective, is that the folks who live there know how good they have it in terms of uncrowded surf, and are determined to keep it that way. They do this by dint of either not renting rooms to surfers [meaning surfers have to make the trek out from Puerto Jimenez every day] or insisting that surfers who want to rent rooms take "surfing lessons", which basically means shelling out an extra $10-20/day. Annoying on one hand, but understandable on the other -- I'd guard a spot like that pretty jealously too.

In any case, this is the spot that we fell in love with the first time we were there, Christmas '02, and is what we were hoping would rescue our honeymoon.

We'd rented the same place we rented on our previous vacation, with the same housekeeper, and were once again met by Mike Hennessy, who both runs a sportfishing operation out of Puerto Jimenez and acts as the property manager for a bunch of the houses that are rented out. Mike is the most permanently stoked person I've ever met [with the possible exception of my friend Ron] -- everything is always awesome, epic and insane. So, of course, when we got there he was telling us how great the surf had been, and was going to be, and how we'd be super-stoked etc. His good mood was contagious and so, finally, we'd arrived at our Happy Place. Right ?

Wednesday, June 22, 2005

MSN Spaces advertising gone wrong

As PZ Myers points out, this MSN Spaces ad is just unfortunate. It's one thing to say that you're not responsible for the contents of blogs being hosted on your servers, but, c'mon, actually advertising a blog that espouses Intelligent Design ? I can just see the headline now: "Microsoft doesn't believe in evolution !", which would be somewhat at odds with their [also somewhat misguided] dinosaur advertising campaign that urges Office customers to "evolve", which, in plaintext, means "Upgrade to the new version of Office, because we need to keep milking that cash cow". [Honesty compels me to admit that, at least with Outlook, they do have a point -- Outlook 2003 is much better than Outlook XP.]

Blergh. Maybe they should stick to advertising blogs that cover things like "What's on TV". Less chance of an embarrassing gaffe there.

Sunday, June 19, 2005

Innocence lost

On the subway, on our way back from seeing "Batman Begins" [which was pretty good, even though the theater we saw it in seemed to be trying to stun us into submission by having the volume turned up to Disaster Area-like levels], we were treated to two very different viewpoints on the continuum of human behavior.

At one end of the scale was the fellow who staggered in, fell into a seat and then proceeded to nearly fall out of it several times. His head [and torso] would start sagging forward, getting to within maybe a foot of the floor and then he'd pull himself back into his seat with a jerk and begin the whole process again. He was clearly feeling the effects of a recreational pharmaceutical of some sort, and it was something stronger than alcohol or weed. Clearly a man with some life experiences, so to speak.

At the other end was the little 5 year-old Hispanic girl that was eagerly showing Christina her jewelry, which included a gold ring on her middle finger. In her desire to make sure that Christina saw her ring, and what was written on it, she made a little fist, stuck up her middle finger, and proudly waved it in Christina's face, all while saying "What says it ? What says it ?", totally oblivious to the meaning usually associated with that gesture. Innocence personified.

I'm sure there's some pithy take-away from this, but I'm damned if I can think of one right now, so I'll just file it under my "Subway as microcosm of human behavior" heading and leave coming up with a Zen koan that captures the lesson contained herein as an exercise to the reader.

Wednesday, June 15, 2005

Theo's Revenge

Yesterday, I accused Mr.Epstein of meddling in areas best left alone. The result:

1. It's 50 degrees and raining
2. Last night, I got the middle joint of my little finger dislocated during taekwondo, making it look kind of like this. Thankfully, a young man who didn't know any better was willing to pull my finger and straighten it back out. From the X-rays, it doesn't look like anything is broken so I just have to keep it elevated, iced and take anti-inflammatories for a few days.

Coincidence ? I think not. I think I'm onto something, and they're trying to silence me. The truth is out there.

Tuesday, June 14, 2005

Paying the cosmic piper

I'm beginning to suspect that somebody, somewhere made a deal with some occult powers: let the Boston Red Sox win the World Series and, in return, you can mess with our environment for a while. Consider: since the Red Sox won last year, we've had a winter that set snowfall records, a spring that set records for rain and cold, a "red tide" that's the worst in decades and is killing the shellfish industry, and now an unseasonably hot and humid start to the summer. I'm waiting for the plague of locusts, or toads to start falling out of the sky.

Personally, my guess is that the person treating with the Dark Powers is Theo Epstein. You don't get to be the general manager of a major-league baseball team at 28 by being a choirboy [actually, in Boston, I think the only thing being a choirboy gets you is some affection]. My theory is that he made his first Faustian bargain to become the GM of the Red Sox, figured "Hey, that wasn't so bad, nobody knows that I now have goat's legs and cloven hooves, let's see what else I can get out of this ol' Cthulhu bugger" and things went from there.

[No, I don't actually have anything against Theo Epstein. I wouldn't know him if he came up and bit me on the @$$. He's just a convenient scapegoat around which to rally any potential villagers with pitchforks.]

Monday, June 13, 2005

Area man thinks WiFi in cafe maybe not such a good idea

The NYT has a post on the ways cafe owners are trying to deal with WiFi squatters, the folks who sit in a cafe for hours on end, revelling in the [mostly free] WiFi access, ordering very little and turning the cafe into a rather antisocial place.

Personally, I never understood the appeal of sitting in a cafe with a laptop for extended periods of time. It seems like the underlying desire is wanting to be around people without actually interacting with them, which is a perversion of the cafe as a "Great Good Place" idea, in which the cafe is meant to encourage interaction rather than stifle it. Laptops really are inimical to interaction;
there's something about being parked behind a laptop screen that's much more isolating than reading a book. Even if you're just reading on the laptop and not necessarily pecking away at the keyboard, that popped-up screen acts as a physical barrier that discourages interactions much more strongly than a book does. Maybe the cafe owners should insist on only TabletPCs being used, with their less-forbidding form factors.

Sunday, June 12, 2005

Brief geopolitical interlude

Summer has started in Boston and I already want it to be winter again. It's 90 degrees, with 20000% humidity, or at least that's what it feels like. Not having an airconditioner, Christina and I have had the distinct displeasure of dealing with that over the last couple of days.

This has led to me to a new theory why there is so much civil war, genocide and general instances of people behaving badly in Africa -- it's because it's so damn hot. I say this because today I was a first-hand witness to how quickly civil war can erupt when it's hot. Christina and I were snapping at each other all day, for no good reason, other than the fact that we were both miserably hot and sticky. We ended up buying an airconditioner and are now sitting in our nice, cool living room, acting like normal people again instead of the snarling beasts we were earlier.

So, rather than all this debt forgiveness stuff [which is of dubious utility anyway], I think new aid projects should focus on "One functioning airconditioner for every man, woman and child in Africa by 2010 !". Doing so would have all kinds of positive side-effects -- they'd have to build better houses [I don't think you can install an airconditioner in the window of a clay hut], they'd have to beef up the electric grid so all those airconditioners would have electricity, they'd have to build better roads in order to get building materials to the power-generating stations and they'd have to educate a lot of people so there would be enough airconditioner repairmen/women to maintain the airconditioners. It'd also be pretty hard for the governing elites to embezzle the airconditioners -- it's not like you can pull up to a Swiss bank with a few trucks full of airconditioners, march in and say "Hi, I'd like to deposit 10000 AC units". And once everybody is nice and cool, the urge to go decapitate your neighbor because [s]he is of the wrong tribe, or is a witch who looked at you funny, or all the other retarded reasons that all this stupid sh!t happens in Africa, would probably be replaced by the much more pleasant alternative of just staying home and being cool.

Vive l'airconditioner !

Honeymoon: Escape from Malpais

[Previously: Malpais, home of the disgruntled expat]

On our fourth day in Malpais, we were once again woken up at an ungodly hour by hammering and a poorly-executed, but nonetheless very enthusiastic, vocal performance. While lolling around listlessly a couple of hours later [it was, once again, raining], we finally vocalized what we'd both been thinking: that staying in Malpais was a sure-fire way of dooming the rest of our honeymoon. Once we'd agreed that this particular elephant was in fact in the room, we started hatching schemes to rescue the week we had left. After thumbing through our guidebook for a while, we decided that the safest bet would be to go back to where we spent Christmas '02, and had a great vacation, namely Matapalo, on the Osa Peninsula. This triggered a round of frantic phone calls, as we tried to arrange accomodations in Matapalo and a flight from San Jose to Puerto Jimenez for the following day. Once we'd arranged all that, it was time to scramble to catch the next ferry. While Christina quickly packed up our stuff, I had the unenviable task of telling the lady running The Place that we were going to depart as abruptly as we'd arrived, and that she'd only be getting 4 days' worth of money out of us instead of the 8-10 days she was probably counting on. [To her credit, she took it reasonably gracefully and was quite prompt about refunding us the extra money once we got back to the US].

We left Malpais at 1pm. The next ferry was at 2pm and 40 miles away, over mixed dirt and asphalt two-lane roads, which meant that I had the perfect excuse for driving like an absolute maniac, especially on the dirt part of the stretch, fishtailing our car around corners in full-on rally style and leaving a mile-long trail of dust behind us. Christina, meanwhile, grabbed the "oh sh!t" handle, held on for dear life and only occasionally whimpered in fear.

We got to the ferry at about 1:55pm, so we thought we'd made it. Unfortunately, we'd neglected to take into account the fact that the ferry had a rather limited capacity for cars, so there was no more space for our car [or the 30+ other cars that had arrived before us and run into the same problem]. The next ferry wasn't until 6 pm, so, there we were, sitting on a ferry dock in the humid Costa Rican heat, with 4 hours to kill and nothing around except a little cantina. Let me tell you, 4 hours is a looong time when you're sweaty and sticky, have already read most of the books you've brought along [and are sick of reading anyway], have had a crappy few days, and are generally disgruntled. As a minor comfort, the cantina did sell cold drinks and ice cream, so we were at least able to gulp down something cold in between periods of sitting around sweating and staring into the distance morosely.

At some point while waiting for Godot, we decided it'd be good to make a reservation in a hotel in San Jose, so we'd at least know where we were going to sleep that night. After consulting our guidebook and carefully picking out a hotel that was supposed to have hot water [a rarity in Costa Rica], I set out to navigate the intricacies of the Costa Rican phone system and make our reservation. This apparently simple task had me stumped for a good 20 minutes because a) I don't speak any Spanish beyond "los pantalones del gato" and b) the notion of a phone menu that allows you to choose what language you want instructions in hadn't quite caught on yet. I'd call the 800 number on the phone card, listen to the instructions [in Spanish, hence totally unintelligible to me], get to the bit where the instructions stop and there's that sort of "Ok, your turn, press some buttons now" expectant pause, key in the phone number to the hotel and be rewarded by another stream of Spanish telling me that I'd done something wrong [at least, I assumed that's what it was telling me, since the call clearly wasn't going through]. After trying that out a few times, I started to slowly do a bit of poor man's cryptanalysis and look for what seemed like significant phrases in the instructions and one phrase that kept coming up was "tecla numero ". I guessed that meant they wanted me to press some magic number, but I for the life of me couldn't figure out what it was. Finally, in defeat, I called the number listed for help and, lo and behold, there was somebody there who spoke English. After I'd explained my problem, she told me the, in retrospect, blindingly obvious answer: I had to press '#' after entering the phone number. That, of course, was the one button I hadn't pressed, being misled by the word 'numero' into thinking that I was supposed to enter a number, not a symbol. The moral of the story: if you don't understand a language, don't assume anything. Alternative moral of the story: when in doubt, press every button you can find until something happens. Unless, of course, it's the Big Red Button.

When the ferry finally arrived, we got on with no problems [it was actually possible to buy tickets in advance this time] and had an uneventful ride over to the other side, arriving around 8 pm. We now had an 80 mile drive back to San Jose in front of us. Under normal circumstances, this wouldn't have been a problem, but of course the circumstances were not normal. It was dark, we had to go over a mountain pass, there were lots of trucks on the road and the road only had 2 lanes. What this meant was that we basically spent 2 hours stuck behind trucks going 15 mph, belching out insane fumes, crawling up the mountain. Overtaking was impossible -- there was a lot of traffic coming the other way, hurtling down the mountain insanely fast, the road wasn't illuminated and there were always several trucks in front of us. I did overtake a couple of times but realized that I was toying with our lives, and that it wasn't really worth it, but that didn't lessen my frustration any. At one point, I got so frustrated that I yelled "F!ck" as loudly as I could, with no warning, totally startling poor Christina, who then had a minor breakdown of her own and demanded that I stop the car and let her out. Since we were in the middle of nowhere, it didn't take much to persuade her that this was an unreasonable request, but the upshot of all this was that our tempers were pretty damn frayed when we finally got to San Jose.

When we arrived at our [very small] hotel, around 11 pm, it looked like it was closed for the night. However, hammering on the door for a while finally resulted in the appearance of a frail, elderly man who'd apparently drawn the short straw and gotten night duty. After dropping off our luggage in our room, we headed out to find something to eat, since we hadn't had a decent meal all day. The only place that was still open was a little dive decorated in rather eclectic fashion, with a mixture of surfing and football [ie soccer] posters enlivened by the occasional wildcard Shakira poster. At this point, though, we were so hungry and tired that aesthetics weren't high on our list, and even hygiene had lost some of its importance -- while we were eating, a cockroach scuttled across the floor and our sole reaction was to look at it bleakly for a couple of seconds, look at each other, shrug and go back to eating.

After wolfing down some greasy arroz con pollo, we headed back to our room, anticipating the pleasures of a warm shower. Ever the gentleman, I let Christina go first. Two minutes after she'd gone into the bathroom, I was treated to a flow of invective that had approximately the following canonical form: "@@@#$!@# piece of sh!t #@$@# shower, the @#%$#%!# water is !@#$!@#*&(^& cold !" When I went in to check on her, it turned out that not only was the bathroom another monumentally idiotic construction that resulted in water all over the floor, but that the @#$@#$%# water was indeed $@#$@ cold. Sighing, I went downstairs to fetch the guy who'd let us in and informed him of our problem. He came upstairs, tried some percussive maintenance by banging on a couple of things with his flashlight, attempted to communicate with the hot water gods by dint of a complicated Morse code sequence of opening and closing the cold and hot water faucets for varying periods of time, held his hand under the water with a hopeful air and then finally informed us with a resigned shrug that there was no hot water, only $@#$@ cold water.

We were starting to feel a bit ... unlucky.

Tuesday, June 07, 2005

Honeymoon: Malpais, the Bad Country

[Previously: we flee to Malpais, over land and water]

After a decent night's sleep, we were awoken rather early by the sound of vigorous hammering just outside our window, accompanied by a blaring radio and out-of-tune singing. When we'd checked in the previous evening, one of the owners of The Place had told us that she had people working around our bungalow but that she'd tell them to lay off; clearly, that message hadn't quite made it to its intended recipients. Oh well. We rolled out of bed, had breakfast and proceeded to check out the town of Malpais, which was pretty easy because it basically consisted of a single road along which surf shops, restaurants and little convenience stores alternated for about half a mile, together with an occasional "villa" for rent, or small hotel. We quickly realized that it was a town that consisted mainly of businesses run by expatriates, people who had come here and gotten stuck, much like Brer Rabbit and the Tar Baby.

After walking up and down a bit, we decided it was time to get equipped for what we'd come to Malpais to do, namely surf, so we wandered into the least-disreputable looking surf shop in search of boards to rent. After fending off enthusiastic attempts to sell us "clothes for the pretty lady", I managed to rent "El Tigre", a 9-foot longboard in a very fetching tiger-stripe motif.

With that, it was time to head for the beach to get my surf on. Now, in order to surf waves that haven't broken yet, you need to get past the whitewater and "out back", where the waves are still just smooth walls of water. On the face of it, that may not seem like a particularly difficult task, but when you have to do this while dragging along a 9-foot plank, it can get tiring pretty quickly. If you're good enough to be able to use a small [6-7 foot] surfboard, you can do what's called duck-diving: as a broken wave comes towards you, you push the board underwater and dive along with it so the wave passes over you. However, the longer the board is, the more difficult it is -- surfboards are meant to float, so pushing them under water and keeping them there takes quite a bit of work. And I had a 9-foot board. Maybe Laird Hamilton can duck-dive a 9-foot board, but I sure as hell can't, which means I was reduced to doing the "turtle": as the broken wave comes towards you, you roll off your board into the water, get underneath it, hold on for dear life and hope that the board doesn't get ripped out of your hands and that you don't get swept too far backwards. Sometimes it works, sometimes it doesn't.

In my case, it didn't -- I spent 30 minutes in basically the same 30-40 foot stretch of water, paddling frantically in between waves only to get swept back towards shore each time, losing all the ground I'd made up. After half an hour of trying to fight the sea and losing, badly, I dragged myself out of the water, a beaten man, to see whether there was any spot along the beach that would make for an easier paddle out.

Christina, in the meantime, had been dealing with unwelcome canine attention -- there was a pack of dogs roaming the beach that had smelled out her love of animals [she probably encouraged them initially ....] and now wouldn't leave her alone. They kept digging holes near her, showering her with sand, and bringing back sticks for her to throw. And they were pretty damn smelly too -- wet, unkempt, sandy dog is a particularly pungent bouqet. For the first time in her life, I think she'd had enough dog-love ... After resting for a few minutes, I waded back into the fray and this time actually made it out. However, I then had to deal with the actual surfing bit and that didn't work out so well for me either. The waves kept shifting, so I was always in the wrong position to catch a wave -- either I was too far in and so it landed on my head or I was on the wrong side to catch it etc. The couple of rides I did get were pretty crappy too, consisting of a couple of seconds on a bad wave followed by a long, agonizing struggle to get back out beyond the whitewater. All in all, I just wasn't feeling the surf stoke, brah ...

The next couple of days kind of blurred together, but the main things that stick out in our memory are:

- The semi-constant rain: as I said earlier, July falls into Costa Rica's rainy season, but we'd been told that the early part of July was the "dry" part of the rainy season. Being the optimists that we are, we assumed this meant no/little rain, when actually it meant "There will be periods of about 2-4 hours when it will be dry ie not raining, giving the rain that fell earlier just enough time to heat up, evaporate and make life very humid and sticky ... but don't worry, it'll rain again real soon". So, to put it mildly, the weather wasn't making life any better since pretty much all we could do in the torrential downpours was sit in front of our bungalow and watch the solid sheets of water cascading off our roof. Good if you're a Zen master contemplating the one-ness of the Universe, not so good if you'd like to be doing things like lounging on a beach.

- Scuba in 60 minutes: one of the expats trying to make a living in Malpais is/was a young German fellow, Toby, who ran a dive shop and offered "express" introductions to scuba diving. Since it was as wet on land as it was at sea, we figured we might
as well go diving and at least have fun while being wet, so Christina signed up for one of the quickie intros. Christina, though, is not a water person -- she maintains [and I must concede that this is a reasonable point] that humans are land animals, that breathing under water is unnatural and that there's really no good reason for putting your face under water. In addition, physics is not her favorite subject. It stands to reason, therefore, that a lecture on the physics of being underwater would go down like a lead balloon with her -- as she sat through the "dry" part of the lesson, during which Toby talked about things like 30 feet of water being equal to one atmosphere of pressure, not ascending faster than 60 feet/min to avoid getting the bends etc, her nods in response to Toby's "Ja, you understand zis ?" got increasingly more desperate. I definitely empathized with her, since it was a lot of material to try to absorb in one sitting [which is why when I got my scuba certification, I did it over 4 weeks =)] but I figured that we wouldn't go any deeper than 20 feet anyway, so it wasn't really essential that she fully grasp what he was talking about.

Once the theory part was over, we headed to the "Swedish" beach, so called because it apparently used to be a spot where topless Swedish women would hang out [so to speak ...], much to the enjoyment of the fishermen passing by. The idea was to start out in waist-high water and get Christina used to breathing through her mouthpiece, clearing her sinuses etc. About 5 minutes into that, it became clear that this just wasn't meant to be -- her mask leaked, kept fogging up and, overall, it just wasn't her bag, baby. She did try a couple more times, though, before declaring herself firmly done with all things scuba and that she was going to sit on the beach. Toby and I looked at each other, shrugged, and decided to go for a quick dive nonetheless. Overall, it was a pretty underwhelming dive -- visibility was bad and there wasn't much interesting stuff to see, though we did run [swim ?] across a turtle and a skate, so Christina didn't miss much.

- Interesting familial circumstances: our hotel was run by two Swiss women, and both of them had a daughter that was somewhere in the 7-9 year-old range. While sitting at breakfast one morning, I overheard these little girls talking about their imaginary [one supposes] husbands. While I thought that it was a bit odd that girls so young should be talking about husbands, the rest of the conversation was even more off-kilter: they were asking each other whether their husbands a) had other girlfriends and b) how many kids they had with these girlfriends. That totally floored me. Seems like they must have had a pretty non-standard childhood to be imagining that kind of scenario while still that young ...

In general, the whole vibe of Malpais was rather depressing -- the weather was bad, the surf was bad, there wasn't anything to do [especially given the lack of surf], the place was pretty much dead in terms of people and the proprietors of the local businesses seemed generally surly, maybe because there were no tourists [other than us] around, and we weren't exactly showering them with largesse.

Thus passed 3 more days of our honeymoon.

Monday, June 06, 2005

Honeymoon: Getting to Malpais

[Previously on Elm Street: we discover the distinct lack of charms of Tabacon.]

After a damp night’s sleep, we lit out at 7am for the long [~6 hour] drive to Puntarenas, where we were supposed to take a ferry. The first part of this drive involved going around the north end of Lake Arenal, on some really, really bad roads [and I’m used to bad roads from Ghana, so that’s saying something] that were pretty much devoid of vehicles. Part of the scenery was nice, though:

In my usual uptight way, I started worrying about what would happen if we ran out of gas, or broke down, while we were in the middle of nowhere – given the amount of traffic on the road, we would have had to wait hours for somebody else to come by. I was somewhat distracted from my fretting, though, by some unexpected roadsigns, like the one for a “German bakery”; given the putative bakery’s location and hence the amount of business they would get, I figured they could probably get by with baking one loaf of bread a year. We also came across a fer-de-lance, a snake whose ideal position is about a million miles away from you. This one was made somewhat less threatening by the fact that it was dead [flattened by a car, from the looks of it], which, to me, is the ideal state of being for poisonous snakes that are within a few feet of me and not in a cage. Not that I have a phobia of snakes -- I've played with pythons owned by my friends and even wanted to buy a snake of my own at one point, but that particular pet portfolio expansion project ran into the parental "Not while you live under our roof" veto. I'm just not a big fan of venomous snakes, which is why I didn’t want to come particularly close to the fer-de-lance even in its flattened state, and so initially just drove past it. About a mile down the road, when it was obvious that I wasn’t planning to stop, Christina asked “Why aren’t you stopping and turning around ?”, in a tone that implied “... you Nimrod”. Exhibiting my flawless grasp of logic, I explained that a) it was a venomous snake b) it was dead c) we’d already passed it and, to reiterate, d) it was a dead, venomous snake and hence I saw no reason to turn around. This chain of reasoning had the predictable effect: none at all. Christina was jumping up and down with excitement and eager to prod it with a stick and go take a closer look at it. After I’d failed to talk her out it, and had turned around and driven back, I decided to be a chivalrous male and let her get close to it first – “ladies first” and all that. After she’d poked it a bit and pronounced it thoroughly dead, I finally sidled over, looked at it for about 5 seconds and pronounced myself satisfied. Here, look for yourself:

Once we made it out of the hinterlands around Lake Arenal and were back on a real road, the rest of the drive went smoothly. We got to the ferry dock a couple of hours before the ferry was supposed to leave, so we had some time to kill. As we were sitting in the car, an elderly man who spoke English with a Carribean accent came up to us and started to warn us about the “snakes” who were apparently hanging around licking their lips [yes, these snakes had lips] just waiting to make an illicit profit off unsuspecting tourists like us. He, on the other hand was, of course, on the side of Justice and Good and, for a small fee, would be happy to watch our car for us. We just nodded politely, agreed with him that it was terrible to be surrounded by such evil, locked our car and wandered off to find something cold to drink and a shady place to sit. This was only partially successful -- we ended up sitting around in a rather hot bar, wishing we were somewhere cooler:

When the ferry arrived, we got to experience the rather innovative ticket-buying system that was in place. There was no way to buy tickets in advance, you had to wait until the ferry had actually docked, at which point you had to run to stand in line at the ticket office, while, at the same time, the line of cars started driving onto the ferry, past somebody who was checking tickets. What this meant was that you a) needed somebody else to drive your car and b) the person driving the car had to point you out in the ticket-buying line to the person checking tickets, in order to be allowed to drive on board. Maybe this was a system designed to weed out the people who were just unfit to be on the ferry, to make sure only the Chosen People got onto the Ark going to the Promised Land. After that bit of excitement was successfully navigated, we were pretty happy to just sit on the ferry and have somebody else deal with getting us to where we needed to be.

The distance from Paquera, where we got off the ferry, to Malpais, our final destination, was about 40 miles, of which the first 20 miles were on decent roads, and the last 20 miles were once again rally-worthy, so by the time we finally arrived at our hotel, we were very ready to be done with travelling for a day. We stayed at “The Place”, a name which I think was either chosen out of hubris [“It’s -the- place to be”] or laziness [“We’re too lazy to come up with yet another name that’s some combination of the words seaside, beach, sun, surf etc, so let’s just call it ... The Place”]. Even though we’d arrived several days before our actual reservation, we didn’t have any trouble getting a bungalow, since, it being the rainy season, there were very few tourists around. The bungalow we got was pretty nice, especially compared with the Tabacon resort horror show we were just coming from, so we settled down to sleep thinking we were about to start having fun on our honeymoon.

Somewhere, somebody was laughing.

Saturday, June 04, 2005

Honeymoon: Tabacrap Resort

After two years of telling the story over and over again, I’m finally getting around to writing up our Honeymoon Nightmare on Elm Street. It’s pretty long, so it’ll be in multiple segments.

Note: unmarried couples may want to consider bringing along a chaperone to reassure them that it’s not always this bad. There will be scenes of graphic disappointment and unhappiness, dashed plans and foiled expectations. You have been warned.

Christina and I got married 2 years ago, in San Jose, the capital of Costa Rica, on the 5th of July, 2003. We picked Costa Rica because we’d been there before and liked it and because we wanted to have a small [pronounced “cheap”] wedding, which would have been close to impossible if we’d gotten married in the US. Having the wedding in a different country made it very easy to justify inviting only immediate family and very close friends without thereby incurring years of wrath from Aunt Maude, Uncle Elmer and Cousin Jeremiah.

The ceremony was held at the Xandari hotel, a beautiful hotel set in the hills above San Jose, in the middle of a coffee plantation. Since Costa Rica’s rainy season runs from May to November, we were a bit concerned about the weather playing along, but it cooperated nicely – it rained all day until the beginning of the ceremony and stopped just in time for the clouds to part a bit and mist to start rising from the ground, making the wedding feel like it was being held up in the sky, among clouds. Or maybe that’s just me putting a romantic spin on it, which is entirely possible, given that I had to grit my teeth during the entire ceremony to avoid bawling like a little girl. In any case, the whole thing went well – we had everybody we wanted at the wedding [other than my dad, who unfortunately couldn’t make it for health reasons], nobody made any embarrassing speeches along the lines of “I remember when Alex used to run naked down the street” [no, I never did that, I’m just making a point] during the reception etc.

Tabacon resort:
A couple of days after the wedding, after we’d said goodbye to all our guests, we went to pick up our rental car and off we went. Our honeymoon plan was to spend a week or so at the Tabacon Resort, at the base of Costa Rica’s [largest] active volcano, the Arenal, followed by a few days of surfing in Malpais, on the Pacific coast. The drive to the Tabacon resort was relatively uneventful, though we did have to turn around once because the road we were on was blocked due to a tree having fallen across it, and nobody was sure when or how it would become unblocked. Part of the trip was over a mountain range, which had scenery that looked like it came out of the Swiss Alps: cows, pastures, twisty roads etc. On that bit of the drive, we ended up stuck behind slow-moving trucks several times and had to indulge in hair-raising overtaking manoeuvers because the road had only two lanes and lots of blind curves; however, that didn’t faze us much because we weren’t in a particular hurry and the scenery was nice [in sharp contrast to a later occurrence of this phenomenon].

When we got to the Tabacon resort, they still had our reservation [yay !] and even went as far as to give us a bottle of wine and a “Love Certificate”, since they somehow knew we were on our honeymoon. The “Love Certificate” made us chuckle a bit, since it was made out not to Mr. and Mrs. Mallet but rather to Mr. and Mrs.Todd, Christina’s maiden name [Yes, I know, we set women’s lib back by having Christina adopt my last name. I lie awake at night thinking about that. A lot. Not.]. That, however, was where the positive aspects of the Tabacon resort ended.

We’d booked a “junior suite”, reasoning that it was OK to splurge a bit on our honeymoon. This “junior suite” ended up being dark [it was a bottom, corner room] and so damp that there was mould growing under the wallpaper. Not exactly the sort of room you want anytime during a honeymoon, but especially not as the first room during the honeymoon, and after the amazing rooms at the Xandari. Poor Christina was so disappointed that she started to tear up, so I valiantly tried to comfort her, but had to admit that it wasn’t exactly what I’d been picturing either. We went back to the reception desk to see whether we could get anything better but were told that that was the best room they had. Hmm. Annoying, to put it mildly. By now, we were pretty hungry, so we figured we’d go get something to eat and would maybe see the room in a more positive light with a full stomach. The resort has two restaurants, one of which is a buffet set next to the hot springs that Tabacon is famous for, so we decided to go eat at the buffet. This turned out to be both a culinary and aesthetic mistake – the buffet was overpriced [$20 a head, in Costa Rica], the food was bad and the scenery was ... unappetizing. And by unappetizing I mean old-hairy-men-with-large-guts-wearing-very-small-swimming-trunks-lolling-in-hot-springs-unappetizing. Bad Naked, all the way. After hurriedly cramming down some undercooked pasta, we headed back to our room to take a shower to wash off the accumulated dust and grime, and, hopefully, some of our bad mood. Alas, ‘twas not to be.

The bathroom in our room was constructed by an idiot unacquainted with two very important concepts in a bathroom: privacy and the dynamics of fluid flow emerging from a showerhead. First, the bathroom was right next to the parking lot – all you had to do was open the wooden shutters and you could touch people walking by. The shower consisted of a showerhead mounted over a circular tub, which was separated from the rest of the bathroom by a downwards-slanting sheet of glass which extended about 3 feet from the wall. The net effect of this was that as soon as you turned on the shower, water sprayed sideways over the sheet of glass and right out the back of the shower and flooded the rest of the bathroom. The water also bounced off the aforementioned wooden shutters, which were mouldy because, well, untreated wood exposed to water will get mouldy. All in all, it made for a rather unpleasant showering experience.

At this point, the thought of staying at the Tabacon for a whole week filled us with sheer terror, so we decided to stay for only one night and then head for Malpais the next morning. We went back to the reception desk and made up a cock-and-bull story about having to check out early because Christina was allergic to the mould in the room [hey, it could have been true, if we’d stayed long enough to find out] and then went back to try to get some sleep in our bed with the damp, musty-smelling sheets. Day 1 of the honeymoon had come to a pretty unsatisfactory end.

Uhm, yeah ... I'm going to have to go ahead and -not- do that ...

Further cementing my conviction that being an academic [or trying to become one] is economically Chewbacca -- Bill Tozier and Bitch, PhD say so. And they know way more about it than I do.