Friday, December 4, 2009

The Seductiveness of Crystals

That's one DnaC protein sticking to another DnaC protein . The dotted lines detail the interactions down to .01 Angstroms (1/1000000000000 meters). Never mind the fact that the actual data on which the image was based has a "resolution" of 2.6 Angstroms.

Your typical protein contains several thousand atoms. To generate these images, the coordinates of all these atoms must be known. That information is normally painstakingly acquired by crystallizing the protein in question, followed by X-ray analysis. There's an element of karma/luck/art involved in generating a crystal; crystallographers can regale you with tales of how they worked fruitlessly for years to coax proteins into a repeating structure, with a drop of spilt coffee proving to be the catalyst that finally gets the job done. A recent Nobel prize in chemistry was awarded to an individual, Ada Yonath, who stubbornly devoted more than 20 years to obtaining her crystal.

More than 60,000 protein structures can be found at the Protein Data Bank. Human DNA only codes for a tad more than 20,000 proteins, but a crystallographer need not fear for his career. You can crystallize proteins interacting with other proteins or ligands. You can crystallize various "isoforms" of proteins. You can mutate your protein strand and recrystallize it. Once you've got the atom-by-atom coordinates in hand, your software can zoom, rotate, label, and color the image. You're an artist. And an explorer, flying over and through the ridges and chasms that might be essential to catalysis.

The work can be important. If you've got a high resolution image of a disease-related protein, it's possible to design drugs that clog it up. It's arguable, however, whether "rational drug design" has come anywhere close to living up to its early promise.

But does this sort of work deserve a Nobel? Does it push boundaries and alter paradigms? Are we talking about extraordinary acts of intellect and creativity? Or just perspicacity?

The questions above are personal, believe it or not. It was flattering to have a professor pursue my services, offering financial inducements, and even pointing out my future lab bench, currently unoccupied. I practically begged for reasons to get excited about the work. I was told of the beauty of meticulousness, the wonders of knowing a subject from the bottom up.

But what about "top down?" Synthesis, integration, binding principles, systems, dynamics, interactions?

The research in question involves a bacterial protein, Cry4a, that is presumed to form a channel in mosquito guts, causing deionization (i.e. death); "presumed" because 20 years of research in labs around the world has failed to prove the point. It would be nice, of course, to benefit humanity by wiping out disease-carrying critters, but...

*Assuming we can engineer a deadlier protein, who's to say it won't get rejected by the bacteria after, say, 1000 generations? The assumption seems to be that a deadlier protein confers greater fitness on the bacteria. Quite naive.

*Assuming a competitive population of bacteria, who's to say the mosquito won't develop resistance to our protein?

*Assuming that resistance doesn't evolve, are we clear about the environmental impact of wiping out a species of mosquitos?

These are "top down" questions. Their answers inform us of the odds that the research might actually be of benefit to humanity. I didn't like the odds. It's possible that some world-beating toxinologists could change my mind. It's surprising, however, that a number of highly respected authorities at my own institute couldn't. There are no vendettas or personal gripes being aired here. I simply wonder a bit about the real state of science in institutes around the world.

Monday, October 12, 2009

Flora and Fauna in Salaya

You can see some more images of my environs here. It's a "" slideshow. I strongly advise against saving pics on photobucket's incredibly counterintuitive, ad-laden website. I do it simply because that's where I've already uploaded a fair number of other pics. It's reasonable to assume would be a better choice.

More pics to come...

Tuesday, September 22, 2009

Alternative Dwellings in Bangkok

Here's a strange dwelling just off Phaholyothin Road, near the Mor Chit Skytrain Station:

Passing by at night, the lights are on. Somehow, just a sliver of a former apartment was preserved in the process of demolition. A parking lot surrounds the structure.

I wouldn't mind living there. Deck it out with vines, potted plants, and eerie lighting.

Here's another joint I've long eyeballed as a possible dwelling:

Cinderella's Castle at the old "Din neramit" Amusement Park. Several generations of Thais have fond memories of this place, as elementary schools would bus their students here for a day of enjoyment. It was hardly world-class and became redundant following the opening of "Dream World."

The park closed about a decade ago, with virtually all the attractions being shuttled off to wherever antiqued attractions get shuttled. Only the castle remains. In the background, you see unfinished condos, victims of the 1997 Southeast Asian currency crisis:

My solution to this double boondoggle:

Wednesday, July 15, 2009

In the course of a day of studying...

...I stumbled across a couple of oddities.

First, there's a web page devoted to documenting instances of left-handed DNA in the media and technical publications. "Handedness" is not a difficult concept. Every nut and bolt and spiral staircase is either left-handed or right-handed. Viewing a spiraling structure from an end (either the top or the bottom), you'll see that the rails spiral away from you in either a clockwise (right-handed) or counter-clockwise direction (left-handed). If a spiral is left-handed when viewed from the top, it will also be left-handed when viewed from the bottom. You can verify that in 20 seconds by twisting up a piece of paper.

The DNA in your cells is right-handed, so any depictions otherwise are in error. The aforementioned website lists almost 700 instances of left-handed imagery, some of which appear in technical papers. The first instance, dating to 1964, was a minor national embarrassment:

(from )

If you want to be finicky, you can point to the rare left-handed form of DNA known as "Z-DNA." In that case, however, half of the "bases" (say, all of the orange and pink strips) would have to be depicted outside the black and white rails, not inside.

The second oddity was this video:

This is farrrrrr from the level of detail I desired. What's more, the video is quite lame from any number of perspectives. But something about the speaker's accent, cadence, focus, and who knows what else, set my brain a-buzzing.

The buzz. Does that ever happen to you? For myself, it occurs when I watch or listen to a person who is intensely wrapped up in whatever he or she is doing. I can recall a couple of instances where the feeling was particularly strong. The first was in watching a cook prepare a hamburger...grilling the buns, treating them with mayo and sauce, gently squishing the oil out of the patties, etc. All accomplished with the utmost TLC. My new-age friends would probably expect such a burger to be especially tasty, with the normally unwholesome, fatty, and carcinogenic properties of various ingredients being negated by the purity of the chef's consciousness.

Another instance was in listening to a speech on the part of a vice-presidential candidate perhaps 20 years ago. Searching the net for third-party candidates at that time, I'm thinking it was Sonia Johnson of the Peace and Freedom Party. Whoever it was, she spoke with strange urgency. If she felt that the audience hadn't fully grokked her message, she'd pause, shift her feet around in little increments, and try to find a new angle of expression. Her gestures were odd, too. Again, a new-age type might see her as a channel for the Truth, with the Truth feeling a tad uncomfortable in that particular body and those particular garments. I wondered if she wasn't a tad nutty. It didn't matter, though, as most of my mental energy was focused on enjoying the buzz.

Anyway, you might want to view the video and see if it produces any odd feelings.

Wednesday, July 8, 2009

Gratawn, Santol

Here's an amazingly delicious fruit that's difficult to find outside Southeast Asia.

The closest thing to an English name for the fruit would be "Santol", from Tagalog. The Thais call them "gra-tawn". You gotta say the first syllable staccato-like.

How does it taste? That's a difficult question. No other fruits come to mind as a reference. Looking at its lineage, you can see why:

Species: Santol Tree (Sandoricum Koetjape)
Genus: Sandoricum
Family: Meliaceae
Order: Sapindales

The Meliaceae family contains about 575 different shrubs and trees, but the Santol is one of the few that produces a fruit of distinction. So, unless genomics proves otherwise in the future, it seems that the Santol is somewhat evolutionarily removed from run-of-the-mill fruits in your supermarket. Moving to the broader category of "order", you do find that Sapindales include ordinary citrus fruits, lychees, and more.

Another Meliaceae that produces edible fruit would be the Lansium Domesticum. The Thais call these fruits "longkang" and the Philipinos "langsat". This is a source for eternal confusion, since "langsat" in Thai refers to a particular variety of longkang. What's more, there's another fruit that we call "longan", but Thais call "lomyai". Not to be confused with loganberries. Longkang and longan look similar, but belong to different botanical families. Longkang are tasty. Somewhat woody. On occasions when I have the will to peel and de-seed the little fruits, I mix lime, longkang, sugar, and gin in a blender. I don't see the appeal of longan, though...they're kind of radishy.

You can see a few similarities between longkang and gratawn. They both have yellow, leathery skin, and a handful of seeds inside. In Thailand, the two fruits come into season in the same brief period...usually June and July. But gratawn are much bigger and taste different. Longkang resin will stick to your hands even after you soap them off, and the pulp will occasionally squirt in your eye. If you let a gratawn ripen fully, however, the flesh is custardy. The seeds are big and tough, so you cut a circle around them, twist the two hemispheres apart, and dig into the flesh with a spoon. The sweetest pulp surrounds the seeds, so you suck on the seeds.

The flavor is...still difficult to describe. Bear in mind that Meliaceae includes frankincense and myrhh and mahogany. There's something spicy going on. I'm guessing that the pulp is loaded with interesting terpenes like linalool, the distinctive fragrance of Froot Loops. When I worked as a chemist at a winery, we had bottle of linalool in the refrigerator. I'm not sure why, actually. Perhaps because the winemaker desired to make illegal midnight flavor adjustments, dripping a few drops into the tanks. Opening a bottle of pure linalool was something like finding yourself in the midst of an exploding Froot Loops factory.

A couple papers suggest the presence of catechins and proanthocyanidins in gratawn...these are more typically found in teas, fruit skins, cinnamon, cocoa, and tree bark.

I just cut a gratawn open...there's something banana-ish in there too.

Unfortunately, I haven't been able to dig up a full profile of the flavor components of gratawn in the academic literature. There are plenty of papers focusing on possible medicinal qualities of the bark and leaves, but no in-depth analysis of the qualities that make the fruit distinctive from an olfactory/gustatory perspective. Sounds like a decent Masters or Ph.D. thesis for someone interested in natural products chemistry.

Tuesday, June 30, 2009

Transformers and Michael Jackson

Normally I refrain from commenting on pop phenomena. This week, however, my brain has reached a state of pop hypersaturation, so I'll blog in the name of self-help.

In college, a friend of a friend (and a distant friend at that...let's get this straight!) was a big Jackson fan and bought tickets for a number of his concerts on the West Coast. Los Angeles, San Francisco, etc. She reported that the show included a segment where Jackson began a song and then ordered the band to stop playing after maybe 30 seconds. You see, his emotions were bubbling over, and he absolutely needed to express them via a different tune. That's nice, but it turns out that Jackson went through this routine at every concert. Offhand, I can't think of a more extreme example of feigned spontaneity.

Some call this sort of behavior "showmanship." Mick Jagger is supposed to be a great showman. When the 40-up crowd (of which I'm a member) ventures out to see a Rolling Stones mega-concert, they inevitably return with high praise - Jagger still has "got it." Then, of course, there are the obligatory comments about Keith Richard's appearance and longevity. To me, it feels like the concert-going fogeys are simply rationalizing their existences; see, us old farts can also prance around a stage. We might just still "have it." Hell, in high school, my circle of friends felt that the Rolling Stones began a downward spiral in 1967, when Brian Jones died. In the early 90's, I was pleased to hear that a decent chunk of the younger portion of the audience walked out on the Stones after a couple tunes. Pearl Jam, it seems, was the opening act, and the contrast between Eddie Vedder's genuine spontaneity and Jagger's rehearsed "professionalism" was too much to bear.

Oliver Sacks relates an anecdote from the aphasic ward of a mental hospital. Aphasics have a difficult time formulating and understanding concepts, so Sacks initially found it odd to see a group of them laughing hysterically at President Reagan's televised speech. As Sacks says, though, "It was the grimaces, the histrionics, the false gestures and, above all, the false tones and cadences of the voice which rang false for these wordless but immensely sensitive patients." Perhaps I lean a tad toward the aphasic end of the spectrum, as Michael Jackson always seemed too cartoony to take seriously. For those who perceive him a master showman, you're entitled to your own personal mix of neurotransmitters.

Regarding pedophilia, I'll give him the benefit of the doubt. Did he fantasize about becoming white?, it seems like he really did have a hangup with vitiligo. I know because I've been dowsed with spam e-mails that prove the point with attached photos. What bothers me, however, is the praise he has received as some sort of music pioneer. Sly Stone and Hendrix were crushing racial boundaries when the Jackson 5 was a generic (but good) Motown act. One might argue that Jackson's transformation into whiteness, like Emperor Leto's transformation into wormness, was an act of sacrifice, designed to carry all sentient beings to a new degree of awakening. But the vitiligo spam disproves that theory.

Then there's the idea that Jackson was responsible for MTV. There may be some truth in that. In which case, the need for a successful musician to have a pretty face, dancing and acting skills, and to be on the cutting edge of fashion and personality - a 30 year trend away from actual musicianship - is Jackson's doing.


Now, let it be known that "Transformers II" is dreck. I just have few observations. In the spirit of the film, they're disjointed.

Following release of the excellent, "Elephant", Gus Van Zant predicted the demise of the "narrative format." No more linear story-telling. That's what you got in "Transformers II", which willfully discards plot and continuity. I say "willfully" because it's impossible to believe that these myriad discontinuities (a robot busts through the wall of the Smithsonian...into a remote jet airstrip) went unnoticed in production. Van Zant's vision, of course, is one intended to challenge the audience. "Transformers II" is the ugly, cynical side of the "non-narrative" format.

In fact, it feels as if recent films like "Star Trek" and "Transformers" operate on the principle that there's no limit to the degree of "suspension of disbelief" that the human brain can tolerate. "Suspension of disbelief" has now been expanded to include much more than run-of-the-mill violations of the laws of physics. We're talking about slashing through a coherent plot and timeline.

I found the first Transformers film notable for its ability to invoke a sense of wonder. That's a rare quality in a film. Somehow, you've got to mix nature, the right music, a sense of connection to the deep past, the grandness of the cosmos, paradox, and death and suffering, in just the right proportions to pull it off. This sense was totally lacking in the second film, a testament to the slipperiness of awe and wonder.

We poke fun at Bollywood productions. Singing, dancing, and fighting. There's something for every audience sector...slapstick for the kids, sex and violence for the teenage boys, true love for the chicks, and family values for mom and dad. But films like "Transformers II" run the risk of falling into the same "variety show" trap. You've got robots speaking with ghetto accents, plenty of slapstick, militarism, and the family pulling through in the end. Unnecessary skits. When Megan Fox's foxiness is the focus, the music changes suddenly, the film slows, and the camera zooms...very Bollywood!

On the positive side, I hope that this piece of garbage forces a number of critics to reassess Star Wars Episodes I-III. Lack of humanity?

Undoubtedly, the execs are rolling in the dough and lighting Gran Coronas with critics' reviews. Prediction: they'll be puzzled when "Transformers III" fails to meet box-office expectations. Hmmmmm.

Friday, June 26, 2009


Google "Pigasus" and you'll find it's a well-used pun. It's unlikely that the Thais at "Satapon Plastic" company were aware of that when they created their logo, however. One wonders what inspired them.

Sunday, June 7, 2009

Western Baggage

He'd already visited me twice, but this time was special. I accepted the sacred text with both hands, briefly leafed through it, then pulled up a chair to place the text on the sahn. Looking back, Khun John began breathing faster and his eyes bulged more than usual. Young farangs are quite excitable. But he smiled and gestured to continue. The little jasmine wreaths were already fresh, so it was only necessary to light the incense and recite a quick prayer. The atmosphere in the room changed.

What did you pray about? I told him that I wanted good luck for my family, refraining from mentioning the means by which this was to be obtained (the lottery). In fact, a glance through the Bible suggested new possibilities for number-selection.

He spoke Thai. Do you believe in God? I reminded him of our English-only agreement. His tone was quite direct today, but the gift entitled him to that. I answered "yes". The flitting motions of his pupils slowed. This was the correct answer. If Tom Hanks had responded this way in "Angels and Demons", he'd have spared himself a lot of trouble.


My respect for the boy had been growing. He was not birdshit farang. His grooming was immaculate, he knew when and how to wai, and sat straight on his two-stroke motorcycle. He had taken vows of sobriety. He worked without hope for material reward in a land far from his own. Our own monks lack such conviction.

It was odd, then, to discover the weakness of his semati. As had become habit, he initiated our session with prayer. It was clear that he was speaking the language of the pra, so there was no point in trying to understand. Instead, I silently repeated a mantra. He had already finished his own incantation, but I felt compelled to continue, as stopping on the fourth recitation would be inauspicious. Khun John stood patiently, exercising the perfection of khanti. The telephone rang. With my eyes only half-shut, I could see him flinch.

What did you pray about (as always)? I really couldn't say, of course, since the syllables were in Pali. I had learned the mantra in my childhood in Isan. We'd take jam-packed song-taews to the wat on auspicious occasions, regardless of the weather. The women would gossip and sing on the way. I salivated over the kanom in their bags. The men hung off the vehicle's railing, still managing to light and maintain cigarettes. Inevitably, the ceremonies had already begun. Everything changed instantly as we shed our shoes and passed through the door. Important work was being done. Oh, I digress...

"You pray and you don't understand the meaning of your prayer?"

A difficult question. Was it a "prayer"? I tried to keep things easy: "Yes, I don't."

"Yes, you do" or "No, you don't"? He muttered something about bananas.

A discussion of English grammar ensued. We agreed that "No, I don't" was the response I had intended. It was difficult to understand the logic behind this mode of speaking, so we both agreed it would be better to memorize the structure and dispense with analysis. "Leave it", as we say.


On our next appointment, he returned to question of belief in God. This time, however, it was "God, creator of the universe." I got the feeling that he conferred with a higher pra; restating questions from previous sessions was one of his patterns. Over time, it had become apparent that believing in this and believing in that was essential to Khun John, so I answered his question as directly as possible:

"I don't know."

From the time of my youth, I had been taught that these sorts of questions were best left to science. He seemed unsatisfied with the response. In some esoteric texts, Mt. Meru is considered the center of this particular universe.

"Do you actually believe that?"


Khun John had the mind of a scientist. He concerned himself greatly with beginnings and ends, sizes and locations, logic and contradictions. He thought a lot.

He had positioned himself directly beneath the sahn. A little chunk of incense broke off and landed on his scalp. The heat was spent, but he sensed a disturbance as he spoke, attempted to remove the particles, but wound up smearing them on his nose and left cheek. For the rest of the session, it was difficult to suppress a laugh. You'd have to have been there.


"What did you pray about?"

This time, I had practiced semati, not prayer. My English was improving. "It wasn't a prayer."

"Well, what did you think about?"

"I try not to think."

"That's impossible."


As it neared time for Khun John to complete his mission, I began to understand. This was a powerful god, capable of creating universes in a fraction of a kalpa. Yet the ten rules and other scriptures showed this god to be subject to the three poisons of attachment, aversion, and ignorance. Jealousy was his strongest attribute; this explained why Khun John would never wai my spirit house, even with his impeccable good manners.

Perhaps this god was a rudra. 6,000 years offer a fraction of the lifetimes needed to reach full awakening, especially via slow paths, so one shouldn't be particularly critical. If, on the other hand, this rudra had a timeless existence (as is sometimes implied), there was really no excuse. Another possibility was simply that this being had incarnated at a high position in the sixth realm, explaining his flamboyant ego.

My English had improved, but I was sad to say goodbye to Khun John. He vanished down the soi, necktie flapping over his shoulder.

Monday, June 1, 2009

A 40+ Farang Going for a Master's

I've been enrolled at Mahidol University for more than a month now, going for a Masters (and possibly a Ph.D) in Genetic Engineering. I had assumed that the relative novelty of a 40-something farang pursuing a degree in Thailand would make for some interesting, bloggable experiences. Unfortunately for this blog, university life has proceeded with few hitches, thanks to the well-organized administration at Mahidol, as well as the mostly 22-24 year old colleagues who don't find my presence the least bit perturbing. 99% of professional travel writing revolves around the pursuit of frustrating, risky, intractable experiences, so I guess I'm a lousy travel writer.

Quitting work has meant cutting back on the luxuries I enjoyed just a couple months ago. No fancy dinners. For the most part, I take the bus or skytrain to downtown Bangkok, something I hadn't done in a decade here, opting for taxis instead. I'm now a "farang kee nok" (birdshit white guy), I guess.

In the name of frugality, I canceled cable TV today. No big deal. It's mostly Korean pop culture, Japanese folks trying to complete some bizarre challenge, Chinese historical dramas, crude CGI flicks involving giant snakes, lanky female humans walking to and fro in garments that are never seen on the street, German language news, endless analysis of soccer, Mexican soap operas, and American professional wrestling. I'll miss the MMA and K1. Boo hoo.

The new routine means a long walk to the Skytrain, dropoff at Victory Monument, and a short bus ride to Mahidol's Phayathai campus. Street vendors. Beggars...mostly blind folks singing with the aid of a cheap amplifier. One dude plays an electric guitar most impressively...I've seen him at Central Mall Lad Prao in the early afternoon many times in the last decade; our routines now intersect more than ever. Others are purely pathetic, victims of mishaps involving electricity or motorcycles. Thais usually don't protest the results of karma.

Coming home means taking the legendary #8 bus. Again, I had no idea about this facet of existence until a month ago. Like most other buses, it's public transport, but somehow this particular number has a special reputation for accidents, folks falling out the doors into busy traffic, and the like. Last month some old guy was hit and dragged under the bus for a couple kilometers before the money-collector noticed thudding noises that seemed out-of-place in the money-collecting realm.

The tour books teach of etiquette on the Thai buses. As usual, the books are nonsense. Seating is mostly first-come first-serve. Unless a patron is obviously frail, few folks will offer their seats. In fairness to the Thais, I don't think the thought process is purely selfish. It's more like this: if I get up and offer a seat, I'll be making myself conspicuous, someone might feel obliged to thank me, and I wouldn't want to trouble anyone that way.

At the Phayathai campus, perhaps 95% of the students are Thai. My first class was something of a prep class for all sorts of bioscience-related graduate programs, so I'm guessing there were 250 students in the room. Four caucasians, myself included. The others come from locations like Indonesia, Nepal, Cambodia, Burma, Iran, Iraq, Egypt, and Ethiopia. It took maybe 10 minutes after the first class session before a dude named Muhammad was offering his views on the role of women (they shouldn't travel), the stupidity of Shiites (versus Sunnis), the decadence of Buddhism, and the amazingness of the Koran. The Muslims, bless their hearts, seem determined to prove that they're reasonable folks and the terrorists are mutants. I already know that, and it's fun to chat with them, but I would also like a chance to chat with the owners of the amazing legs that are only seen at a tangent.

Sarbast, a Kurdish Iraqi, is a fun dude. He doesn't hate the American soldiers, but does find them odd. Why, he laughs, do the soldiers purchase so much Viagra from his pharmacy when prostitutes are fairly scarce (though hardly nonexistent) in the region? The massive consumption of anabolic steroids is more understandable.

I'm mostly impressed with the education I'm getting so far. The profs are Thai, but their English language skills range from adequate to flawless. Acharn Prapol speaks with a fairly strong English accent. As might be expected, there's a slightly heavier emphasis on memorization and testing than you'd probably see in the West, but it's not as if the profs don't understand the importance of communicating broad concepts.

Below...9 of my 15 compadres in this year's Genetic Engineering program, eating noodles near Victory monument.

Sunday, April 19, 2009

oo (อุ)

That's a bottle pot of "oo", an alcoholic treat from the Northeast of Thailand. I paid 160 baht for it...about $4.

"Susan Boyle Mother Tong Yaem" brand. Don't drink and drive. It's illegal to drink if you're under 18. Expiration date. Etc.

You've got to bust through the plaster seal before you can drink. It's a pain in the ass. It was the second time I tried the stuff, so I knew what to do...bring it down to a local eatery and let management deal with it.

Rice husks. I'll have to do some more research on the topic of "oo", as the stuff is still a mystery to me. Alcohol is a liquid, but it seems like the contents are not the least bit moist. You add water, wait 5 minutes, punch the wooden straws through the mass (difficult!), and suck.

Tasty stuff. Sweet and sour. You might compare it to sweet sake or, if you're already familiar with Thai alcohols, "sato". I'd say that it's more complex than either, however. I detected hints of cinammon and/or coconut, though I doubt any was added. Apparently, you can get "oo" in pineapple and watermelon flavors too.

It's not easy to find oo in Bangkok. This pot was acquired in roundabout fashion: a couple weeks ago a taxi driver and I found ourselves chatting on the subject of oo. He actually went out, bought a pot, and stowed it in his trunk, waiting for our next encounter. I threw in a 40 baht tip for the effort. He told me he found the stuff at an "OTOP" (one tambon/village, one product) shop in Bangkok.

Befriended taxi drivers, by the way, are awesome resources. I can't count how many times I've hopped in a taxi, told the driver to "take me to a good Thai restaurant", and had a great meal.

Sunday, March 29, 2009

The Mantra of Avalokitesvara

How does a denizen of the Nepali Himalayas become affluent in a non-touristed region? Join the Indian army. Send the money home to your devoted wife, who purchases a TV and satellite dish, solar panels, Tibetan carpets, thangkas, and various adornments for the shrine. A large poster of an English manor and flower garden...true paradise. A sink and an improved hearth. Copper pots. A comfy bed. And a high quality sound system.

Thus it was that I found myself in a surprisingly clean and well-managed tea house in the non-touristed Ganesh Himal. In the early evening, hail pounded down on corrugated metal roofing, a good time to slurp Tibetan tea and rakshi.

At 6:00 AM, I was blasted out of a cozy sleep via the above Mantra of Avalokitesvara, piped directly into the sleeping quarters. The reaction was irritation. I paid good rupees for my sleep. Those feelings dissipated quickly. The sky was clear, the Himalayan foothills green, prayer flags flapping in the breeze, and the villagers were an hour into their routines. This rendering of the Mantra is mind-blowing, as far as I'm concerned.

Some folks, mostly Westerners, describe this take on the Mantra as "new-agey" or "inauthentic" or "over-produced". You wouldn't have heard this melody wafting out of Himalayan gompas 15 years ago, much less a century. The instrumentation is not entirely Tibetan. That doesn't stop lay Buddhists, and even some Hindus, from dropping the cassette into cassette players (no iPods as yet) as they trod through the mountains, rewinding every 23 minutes and 55 seconds. The tune, if it can be called that, emanates alongside juniper and pine incense from shops in Boudhanath, Thamel, and elsewhere in the Kathmandu valley. I feel a tinge of pity for anyone who fails to be transported.

Tuesday, February 24, 2009

On the Falsifiability of Evolution

I would give absolutely nothing for the theory of Natural Selection, if it requires miraculous additions at any one stage of descent.

Charles Darwin (in a letter to Charles Lyell)

To reject one paradigm without simultaneously substituting another is to reject science itself.

Thomas Kuhn (The Structure of Scientific Revolutions)


One of the websites I most love to hate, "Uncommon Descent", has a post regarding the falsifiability of evolution. Many "intelligent design" proponents (IDiots) are sophisticated enough to claim to concede "common descent", so the poster argues that biologists can't simply invoke Haldane's "rabbit in the pre-Cambrian" argument to drive a wedge between evolution and ID (as the discovery of a rabbit in the Cambrian would falsify both views).

What numerous ID proponents seem to argue for is "common descent with meddling", the meddling being of a conscious nature. But is that really common descent? Such a view suggests discontinuity, which could/should manifest in the fossil record. When arguing with "common descent with meddling" advocates, why shouldn't a "rabbit in the pre-Cambrian" be invoked as a falsification of evolution and a confirmation of ID? The rabbit is admittedly a dramatic example of discontinuity, but it differs with myriad other possibilities (e.g. a mammoth in Australia) only in degree. When an IDiot says that evidence for common descent can never refute ID, an appropriate response may be, "what bizarre version of common descent are you imagining?" Ordinary sexual/asexual reproduction plus occasional/constant creative input from a third/second party designer is quite a distortion of the historical concept. Visualize a "tree of life" with disconnected branches held up by skyhooks. Alternatively, you can place a fairy on every fork.

Another ID view, the front-loading view, is that evolution was somehow programmed from the very beginning to be driven, or accelerated toward some end; a single, primordial instance of meddling. Here, a "rabbit in the pre-Cambrian" would clearly falsify both this view of ID and evolution. So how does a researcher falsify either of these views? I'd say that the IDiots are playing a sneaky game here: they do their damndest to conform to standard theory, sprinkle in a tad of supernaturalism/teleology, and then ask biologists to falsify one view over the other.

Obviously, the more closely a parasitic view wraps itself around the other, the harder it is to falsify one view while leaving the other intact. Given a choice of views, it seems eminently reasonable to opt for that which is supported by peer-reviewed research, practicing biologists, and which dispenses of superhuman entities. Tediously, the "Uncommon Descent" crowd spends a great deal of energy refuting this, invoking worldwide academic conspiracies, the wisdom of engineers who aren't constrained by mere biology, and the Designer Without Inferable Motives or Identity.

Above, one sees that ID takes a number of forms. The rabbit in the pre-Cambrian falsifies some versions, but not others. But proponents like Dembski and Behe fastidiously avoid formulating specific theories of ID, preferring to harp on every perceived weakness in standard evolutionary theory. They wouldn't want to favor the frontloaders versus the tinkerers versus the constant interventionists versus the creationists. At the same time, when arguing that evolution is difficult to falsify over ID, the IDiots can conveniently pull out the version of ID that best makes the case.

Given the fact that some versions of ID are hugely parasitic on standard theory, piggybacking, free-loading at every opportunity, biologists are sometimes challenged to show how evolutionary theory provides any practical benefits that competing "theories" couldn't. The responses of biologists run the gamut, from Dobzhansky's famous "nothing in biology makes sense except in the light of evolution", to Coyne's recent argument that evolutionary theory, like cosmology, need only expand human knowledge to justify its existence.

Personally, it does seem that hardcore biologists sometimes exaggerate the case for evolutionary theory's utility in a clinical setting. A compartmentalizing creationist crystallographer could conceivably concoct cofactors (sorry, couldn't resist) that inhibit enzyme function, believing all the while that the active site was the result of conscious design. However, it occurs to me that one area that ID, in most of its incarnations (we can never say "all", given ID's aforementioned slipperiness) would fail horribly is in that of "ultra-selfish" DNA. We're talking about transposons, retroviral sequences, etc., that function solely to perpetuate themselves through the host's DNA. These sequences are problematic for ID, as they confirm an abundance of "junk DNA" in the genome, something most IDiots dispute with great tenacity. At the same time, these entities are strongly implicated in cancers and other maladies. Certainly, modeling and proposed treatments for such disease pathways should be influenced by whether the sequences are primarily "selfish" or "functional". To simplify, in one case it might be possible to "attack" the sequence and its [selfish] activity; in the other, one would expect any number of side effects.

My own dogma is that scientific insight arises in the minds of those who are already strongly grounded in correct views. Is it any surprise, then, that "ID theorists" contribute nothing to biological understanding?


Below, I'll try to collect articles that do support the utility of evolutionary theory in medicine:

On the Utility of Evolution in Experimental Biology and Medicine

Hacking Evolution

Of What Value is Evolutionary Biology in Medicine?

Evolution as Policy, not Symbolism or Critical Thinking

Does Evolutionary Biology Make Predictions?

Of course, I understand that the poobahs of "Intelligent Design" may not be impressed. They'll argue that they don't deny "microevolution", so evolution of antibiotic resistance is no proof of standard theory's superiority to ID. They'll tell you that experiments in synthetic biology are an example of design, not evolution. And, of course, medical inferences based on "common descent" are taken to be "exactly what ID predicts".

The lack of creativity of ID proponents is sometimes mind-blowing. In addition to the aforementioned inability to come up with their own theories and research, there's the consistent flow of arguments that boil down to incredulity...I can't imagine it, so it can't be true. There's also this childish tendency to try to parrot back the criticisms of their opponents: evolution is a religious belief, evolution requires too much faith, blah, blah, blah. This is the tact adopted by children who, having been insulted, can't conjure up a decent comeback.


Click here for a more artful "rabbit in the Cambrian" image.


Sunday, February 15, 2009

Samak's Nose

Above is a shot of former Thai Prime Minister and Bangkok Mayor Samak Sundaravej. He had some highly lampoonable quirks, as you'll see.

Amongst numerous segments of Thai society that reviled him were the artists. That's largely because of his efforts to open a shopping mall/car park where an art museum had been planned. To Bangkok's benefit, the artists ultimately got their way. Way back in 2001, however, things were up in the air, and the artistic community staged a protest event. Participants were given canvas and paint. You can now see hundreds, perhaps thousands, of their efforts on the top floor of the art museum.

Samak was a cat fancier. The fish represents the museum. "Cats eat fish; the mayor eats the art museum". In English, we don't really have a slang word for "eat". In Thai, however, the word "daeg", used in the work, is considered quite nasty. These artists weren't pulling any punches.

A five minute browsing of a guide to Thai etiquette informs you that you should be careful where you point your feet. Samak is represented as the red foot above, squashing hopes for a museum. How do I know that the red foot represents Samak? Read on and take a second glimpse at the pic.

The above pic actually takes a swipe at foreigners: "Black head [like a real Thai], face like a foreigner". Apparently, a Japanese consortium was behind the shopping mall efforts.

The pic above references Samak's TV cooking show. The translation is a bit tricky...something like "we want an art museum; don't eat it you stupid man".

"Evil mind, Evil thoughts, Evil culture".

Now, if you haven't already noticed, all the pics target Samak's distinctive nose.

More nastiness. The nose, which needn't even be embodied anymore, is also given the attributes of a buffalo. More so than any other animal (with the possible exception of a water monitor), you shouldn't liken a Thai to a buffalo. It's the sort of offense that could earn you a punch.

Adding another level of abstraction, the nose takes the form of a rampaging rose apple!

Above is just a small selection of the works.

Google "Samak's nose" and you'll find that TV sign language interpreters simply touched their noses to indicate "Samak Sundaravej". Though the translation had persisted for a decade, some of Samak's supporters caught on and protested. To quote one article: "Stung by the controversy, the association [for the deaf in Thailand] has been examining other ways to indicate Mr Samak, for instance a reference to his passion for cooking."

I'm not sure how sign-language interpreters now refer to Samak.

Saturday, February 7, 2009

3,2,1 Buddhas

(The last one is a friend's pic, actually)

Friday, February 6, 2009

Tom Yum Poong Plah (Thai Fish Maw Soup)

My dinner Thursday night!

Below you see "Plah Deuk Foo"...shredded and deep fried catfish. Properly prepared, it's not nearly as greasy as you'd expect. It's standard fare. Often, it's served with mango yum, which cuts through the oiliness. This time, though, there's a kind of curry sauce. A nasty, cheesy aroma wafted off it. They actually added milk to the sauce...a bit unusual in the country where the populace has the lowest lactose tolerance in the world.

The next course is "Yum Gorp". Chilis, spices, and frogs! The blackish blobs are the frogs. In a Thai restaurant in the USA, where the waiter might ask you to specify your spice-tolerance on a scale of 1-10, this would rank 100.

Next is "Gratai Put Pet". Rabbit. The green spheres are fresh black peppers.

Take a moment to grok that pic. It appears primed to spontaneously ignite. I've been here long enough to derive honest masochistic pleasure from extreme spiciness; nevertheless, it would be nice to actually experience the rabbitness of that rabbit. You can slosh some beer around in your palate and launder the remains of the critter, but it won't help much.

Here's the real treat. It looks innocent enough as it's placed on the table....

But there are some jewels under the placid surface...

Tom Yum Poong Plah...Thai Fish Maw Soup (ต้มยำพุงปลา). That veined, maggoty entity is an egg sack. I think.

Just to be sure, we asked the waiter if everything in that bowl was edible. "Mai mee kee", he said ("no have shit"). Reassured, we dug in.

For foreigners who straddle the border between novelty-seeking and health concerns, Thais almost always remove the shit from the fish they serve. The exception would be small fish, where the diner must perform the "shit-ectomy" with fork and spoon.

It's not subtle. It's not French cuisine. But it IS gamy, spicy (to an extreme, if you're unaccustomed), complex, and intense. You sweat and drink beer at a high flow rate. It's hard to imagine legally available food products eliciting more sensation per neuron.

It would be all the more amazing accompanied with, say, some trance-inducing "Mor Laem" music. But, of course, management sees the farang enter the joint and promptly whips out a selection of Abba and Carpenters tunes. Oh well.


I just showed these pics to a Philippino friend. She then proceeds to tell me about cow testicle/penis soup. Apparently, you simply ask for "Soup Number 5", and everybody knows what you're talking about. Of course, it's supposed to increase virility. Sometimes they even throw in a sea cucumber for extra phallicity. Are there any dishes that perform the opposite function? Boiled eggplant?


On second thought, maybe the choice of music wasn't entirely inappropriate.

Tuesday, January 20, 2009

Mud Muse

In the early 70's, my parents dragged my siblings and me off to a kinetic art exhibit at the Los Angeles County Museum of Art. In retrospect, it's surprising that this opportunity ever arose, as my parents aren't exactly connoiseurs of this scene.

On arrival, we were greeted by a giant, undulating ice bag. It might have been 20 feet high. (Note 5/31/2009: click on the link and you'll see that it's not 20 feet much for childhood memories). Bearing in mind that my memories are dim, I certainly wondered "what's the point?", and probably didn't get any satisfying answer.

Inside the museum, the first piece was a snooker-table sized tub of slowly gurgling, bubbling glop. A plexiglas window prevented most of that glop from going splat on the art aficionados. There were occasional major eruptions, however; the evidence was all over the floor.

I didn't want to leave that room. "What's the point?" didn't have much point at that point. You'd just strain your little head to catch the next explosion, mesmerized by the whole messy affair.

Onward to a pre-laser light show. After that, I don't recall. I assume we ventured into other, more permanent exhibitions. We may have passed by Van Gogh or Picasso. Or Warhol, for that matter. The art that left a lifelong convex-shaped impression, at least until I go senile, was that tub of mud.

A few years ago, I got to wondering what exactly I saw. Turns out, it's "Mud Muse" by Robert Rauschenberg. He died just last year! Quite a famous figure, if you know your modern art. Along with Jasper Johns, Warhol, Twombly (friends and/or lovers, actually), the stereotype of the whacked-out modern artist.

I asked my father about that exhibition. He retains a sort of catalog of all the pieces at the event. More than 200 pages. The construction of "Mud Muse" is covered in a fair amount of detail. The "mud" is actually bentonite, known best to me as a protein-removing substance in winemaking. The gurgling was caused by some sort of vibrating action under the table, not a conventional system of pumps.

Google "mud muse" and you'll read the art critics a-cooing. According to one, it's "the interactive work of art conceived as the perfectly responsive lover." OK. Others make note of the fecal texture and color of the work. Even as a toddler fresh out of his anal expulsive phase, I don't think I saw things in that light. It was just the essential, amplified, glorified gloppiness of mud.


Below is a video of "Mud Muse" in action. I don't recall any soundtrack, and have a strong recollection of the mud being far more viscous. Perhaps someone over-diluted the bentonite on the day the video was shot.

Monday, January 12, 2009

Yum Kai Mangda

An American friend once described a horseshoe crab as culinarily useless. Not true, as you can see. Those orange globules are the eggs of one of the critters, served up with onions, chilis, mangos, and the other sorts of ingredients you typically find in Thai "yum".

The experience is something akin to eating little nuggets of candle wax. That's not a complaint, actually, as the resulting texture is unique. As with any number of other Thai dishes, there's an element of "sanook" (fun) involved in the gustatory process. It begins when the appalling form of the "mangda" is presented on the table, continues as you endure the spices, and nears completion with those little spheres rolling about in your palate.

Now, don't start combing the nearest beach for these buggers. For one thing, there are some conservation issues. More immediate, however, is the fact that the eggs of certain species are loaded with tetrodotoxin, the same poison found in fugu, the famous Japanese pufferfish. A Mahidol University paper counts 280 cases of poisoning, including 5 deaths, between 1994 and 2006. In Thailand, the culprit is the species C. Rotundicauda, as opposed to the edible Tachypleus Gigas. The appearance of the two is quite similar.

It's a tad difficult to hunt down this dish. A couple of the aforementioned deaths were fairly recent and well-publicized, so restaurants and customers are a bit wary. You could start by avoiding the sorts of joints that have large numbers of tourists. Also, smallish eateries probably won't have the kind of customer volume that justifies purchasing fresh horseshoe crabs on a daily basis.

Did you know the mouth of a horseshoe crab lies between its legs? Another interesting factoid: the beasty is more closely related to spiders than crabs, shrimps, or lobsters.

Tuesday, January 6, 2009