Big Hand = Small Banana ???

The Seven Things You Can't Doo in a Thai Taxi

Alternatively, this post could be titled, "Just as I was about to crap in the taxi..."

In case you're wondering, image #6 is a durian fruit.

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.

Flora and Fauna in Salaya

You can see some more images of my environs here. It's a "photobucket.com" 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 flickr.com would be a better choice.

More pics to come...

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:

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 http://www.ccrnp.ncifcrf.gov/~toms/icons/stamp.israeli.1964.jpg )

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.

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.