Friday, December 13, 2013

Glad that's off my bucket list

I've been obsessing over this difficult-to-find fruit for the last couple of years, like it might be the last in a series of bizarre fruits which, when eaten, unlock immortality.  My friends and I were engaged in a "have you ever eaten XXX?" conversation, and this one was missing from my list.  In Thai, it's "ma-kwid"; in English, "limonia."

It's not delicious.  Cheese, yeast, and bread aromas wafted out, overpowering some more subtle ones (vanilla, perhaps) and that's not because the fruit was rotten. There's some sweetness there. The seeds are edible and crunchy. The best comparison in my mind would be to tamarinds, but apparently it's more closely related to ordinary citrus fruits, like oranges. Psychologically, the color and mushy texture doesn't help its appeal, of course.

Monday, June 10, 2013

Lynched Openbill

Sorry about the quality of the image.

I found this situation a bit too surreal to ignore.  It's an Asian Openbill.  It appears that the bird met its death by hanging. Adding to the bizarreness is the cross-like feature on the rope or branch.  The critter has been up there for several days now, surveying the rice field, ignorant of the thunderstorms.

Monday, June 3, 2013

Rove Beetle Brushup

Above is the result (on me!) of barehandedly killing a "rove beetle."  They don't bite, they don't sting, but their internal juices contain a nasty chemical.  As with poison ivy, the discoloration tells the viewer where your hands journeyed shortly after the initial contact.

It's more of a stinging sensation than itching.  Not a big deal.  More than anything, I'm not thrilled about the prospect of repeatedly explaining what it is and what it isn't (NOT herpes!) over the next week...there's a mark on my face, so there's no hiding.  But if you google for references to the rove beetle, you're like to find superlatives like "extremely painful" and "more potent than cobra venom."  I wouldn't trade 1,000 brushups with the rove beetle for one cluster headache.

The Thai term for these buggers is "duang gon gradot", which translates to something like "ass jumping beetle."

Saturday, January 14, 2012

Thoughts on the Thai Flood

If you follow the international news, you know that parts of Thailand were deluged from October through December. I'm not sure the scope of this mess is appreciated, however. The total damage is estimated to be over $50,000,000,000. For reference, hurricane Katrina boasts an $80,000,000,000 figure. Consider, though, that Thailand is nowhere near as wealthy as the U.S., and the flood affected a large % of the Thai populace.

I've been through a couple major earthquakes and a fire. Floods are different, I can now say. In the recent case, at least, the water continually rose over a period of a month. First, the water creeps up to the level of the road. Then I found myself bicycling through a foot or more of water to get to the University. When the water began to enter the house, it was time to find a new dwelling. Like many others, I assumed it would just be a week before I could return, so I didn't bother to move my refrigerator, washing machine, etc., upstairs. Other folks fared worse, leaving their cars and motorcycles behind. Three weeks later, I returned in a "long tail" boat to survey the damage. In a village of 100's of townhouses, I saw maybe three faces. Inside the house, black, stagnant water. I had been told that the village management would turn off all electrical power...I discovered this was not true when I interacted with my refrigerator, floating, but tethered by the electrical cord.

All my previous experiences with long tail boats were in paradise, Southern Thailand. And, in fact, the one hour sojourn was quite pleasant, winding through palm trees and abandoned properties. I had to laugh.

Vandalism was being reported, so I pulled my hard drive and other valuables. Apparently, a crocodile was caught in the village.

Then, as the water recedes, the aforementioned events play out in reverse. The symmetry is broken, however, by death (my plants!) and filth that wasn't there a few months prior. It turns out that children's items are particularly floaty...thus a huge stash of shoes and plastic toys in my corner of the village. A pink plastic hobby horse with wheels. Large stuffed animals, including a smiling tortoise. The requisite tire. Endless plastic bags, garden pots, bottles, etc.

My camera was also a victim, so I regret that I can't show you the tortoise happily surveying the damage. My new camera can only capture the latter stages of this mess.

Snail eggs, stuck to my wall. It's amazing how fast these buggers, a bit bigger than ordinary escargot, propagate, infiltrate, and die.

Above is my lovely sewer. Over a couple of months, fish invaded every conceivable space. Now they're floundering around in whatever water they can find. This one's dead, but there are living specimens in that filth as well. See the pink toy?

My only surviving tree. Everything else is dead, including a mango that produced exactly one exceedingly delicious fruit in its life.

It wasn't advertised, but apparently these homes come with self-cleaning walls...exposure to the water causes everything to peel off. The dirt on the washing machine gives you an idea of its position as it floated around the interior. Unlike my refrigerator, it still works.


Everyone, including me, observes that 2011's rainfall didn't seem much heavier than 2010's. There are 100 theories as to why this disaster occurred. As things go in Thailand, it's unlikely that a clear picture will ever emerge, particularly if some important people are to blame. Some blame the minister of the interior for his decisions regarding management of dams in Northern Thailand. The idea is that poor choices were made in the name of populist politics, aiming to please the farmers in the northeast of Thailand by retaining excess volumes of water. If so, the cost of a few folks' politically-motivated resource management decisions is almost inconceivable.

Though there's no evidence for it in this case, I note that Thai politicians are very much in the habit of timing events and making decisions based on astrology, numerology, feng shui, etc. I wonder if superstition played any role in this monstrous mess.

Friday, January 13, 2012

Buddha and Bobbing-Head Snoopy

In case it's not obvious, that's a fat Buddha hanging out with two bobbing-head Snoopies on the carpeted dashboard of a taxi. In the Thai mind, there's nothing horribly incongruous about this arrangement.

It's a watercolor. I guess I cheated...the painting is based on a photo, which was then photoshopped, printed out, reproduced on tracing paper, and copied onto watercolor paper. From there, it's about as difficult as filling in a child's coloring book.

Sunday, April 17, 2011

Salmon Sperm DNA

You might be surprised at how important this stuff is in the biosciences. It's used as a "blocking agent" in Southern blotting, a common method for identifying a DNA of interest in a forest of DNA molecules, and as a "carrier" when trying to introduce DNA into yeast. DNA tends to interact with DNA; in cases where you want two kinds of DNA to interact in a general, not entirely specific, manner, you want DNA that comes from a species that isn't closely related to the organism you're working with. If you're working with human DNA, salmon sperm DNA will fit the bill. If you're working with salmon, of course, you'll have to find another source of DNA. In European genetics labs, you'd be more likely to find a bottle of herring sperm in the freezer.

You also want a relatively cheap source of DNA. Male salmon release their load into the water, so they need to make a lot of the stuff. As is the case throughout the animal kingdom, sperm has a high concentration of DNA (i.e. the cell doesn't contain much more than a nucleus), so it's a good source of DNA.

The dry flakes are difficult to dissolve in water, so you've got to boil the stuff. I had to prepare a few milliliters last weekend. Oddly, after all the processing and purification it took Sigma Labs to put 1 gram in a plastic bottle (at about $100 a pop), the distinctive aroma of salmon permeated our lab upon boiling.

Interestingly, if you examine the history of DNA science, salmon sperm has played an important role from the very beginning. Crick and Watson figured out the structure of DNA, but a dude by the name of Friedrich Miescher worked out its basic chemistry nearly a century prior. You can read the story in detail. Miescher, apparently, did fine and meticulous work, and understood that this substance ("nuclein", back then) must be of importance in the cell.

Salmon sperm (from the Rhine) provided a good source of DNA for Miescher's studies. Back then, if you wanted to characterize some chemical, you'd heat it and boil it and torture it, trying to register a weight change in, say, a phosphorus-absorbing substance. That way, Miescher worked out that DNA is 3% phosphorus. Needless to say, that approach required copious quantities of starting material.

Since sperm is mostly nuclei (which is where the DNA resides), it made sense that it was involved in fertilization. Given the techniques of the day, though, it seemed that nuclein from salmon was no different than nuclein derived from any other organism, so Miescher looked elsewhere for the genetic essence, even speculating that the chiral nature of protein might hold the key (40 chiral centers in a protein mean 1,099,511,627,776 arrangements!).


Did you know there's actually a disease, trimethylaminuria, where the patient gives off a fishy odor? According to Wikipedia, "Living with TMAU can be challenging, and TMAU can adversely affect the livelihood of the people who have it, as well as their families." Yikes!

Sunday, September 26, 2010

What Have I Been Up To?

I haven't posted for a while. That's because I've become obsessed with my work in the lab, to the neglect of other aspects of life; a real lab rat.

When folks ask me to give an indication of my pursuits in the lab, it's often difficult to respond. As with many fields, layers of understanding are built on layers of understanding. How does one simplify this knowledge for the non-specialist? Well, with the aid of Joan Miro ("Harlequin's Carnival"), I'll try.

In the realm where humans operate, manipulating objects in a narrow range of size and mass and speed, mostly in a gaseous medium, keys don't spontaneously diffuse into locks, opening doors, allowing 100,000 balloons to occupy the room. The balloons are then not removed by grasping tendrils that emerge from the wall sockets, and all the above doesn't occur in less than a second.

But appearances change a bit in the tiny, enclosed, fluid environment of a cell. There, the size of a water molecule actually makes a difference. It's zigging and zagging at about 600 meters per second. Some say Einstein's observation of little pollen grains getting zigged and zagged by the zigging and zagging of water molecules ("brownian motion") was the final proof of the existence of atoms.

Bigger items like proteins and DNA also zig and zag, just more slowly. A reasonably sized protein might cover 1 meter in a second. That's still outrageously fast for something that's bottled up inside a space that human eyes can't perceive.

The universe inside the cell is also one of exquisitely tailored shapes of a huge range of stickiness. Whereas a high speed collision between two cars often results in death, destruction, and freshly-unusable parts flung in every direction, a collision between two proteins can initiate a chain of events that does something useful. You might imagine Miro's disembodied hand having a particular affinity for the window latch. Having twisted the latch, the window opens. The hand has no affinity for the latch once the window is opened, so it releases its grip. The little harlequin dude releases the cat-figure, which closes the window, which spontaneously latches, and then the disembodied hand performs its role again. This could repeat, say, 10,000 times in a second.

I should emphasize that there's a huge variety of stickinesses inside the cell. In our tedious realm, there's the stickiness of masking tape, the stickiness of gravity, and a few other sorts of stickiness. In the cell, though, you might have rules like "fish only interact with items found on the table, never elsewhere." And the cone can only stick to a perfectly cone-shaped hole in the wall.

There's a lot of stuff I'm ignoring here. What's to prevent events occurring in reverse? What powers all this motion? How do things change, say, if the disembodied hand gets tethered to the wall? What's going on in the next room? That's OK.

Point is, the universe inside the cell is one of interactions. I suppose the typical interaction between components in the cell is one of total indifference, the ladder not giving a crap that the dice just rolled into it. But the "productive" interactions are frequent enough to make all the difference. Some branches of modern biology (e.g. "systems biology") seek to understand the complete cell in terms of all these interactions. It's a huge task, with maybe 50,000 different proteins and RNA molecules, and a couple meters of DNA in your cell, all jostling and interacting with various degrees of stickiness. Part of me rebels against this mechanistic view, but I don't see a reasonable alternative. At some point in the future some commentator might scold this generation of biochemists for ignoring the "weak" (but frequent) interactions, but that would be wrong; it's hard enough to document all the strong ones right now!

There have been some amazing and inspiring animated attempts to simulate the life of a cell based on real knowledge of shapes and interactions. Such videos, however, can't possibly convey the speed at which these events occur. Nor do they show the myriad random, unsuccessful interactions that occur for every productive one...thus it appears that components are actually being attracted together, magnetic-like, over long distances. That's not the case.

So now, to move away from Miro and the abstract, what I'm trying to do is this: identify all interactions between human proteins and the RNA of a particular virus. Viruses aren't like Arnold Schwarzenegger announcing his presence with a minigun. They do their best to merge with the crowd, making it difficult for the cell to detect any unusual interactions. We're using a technology called the "three hybrid system." Basically, a protein latches to both DNA and RNA, and if that RNA latches onto another protein, that protein will latch onto another protein, which will make a different kind of RNA, which will interact with a ribosome and get translated into a new protein, which will interact with a small molecule and turn the yeast cell blue. The blue color, in turn, makes me happy. With the help of numerous other interactions, of course. I'm still boggled by the fact that the system works at all. There would seem to be too many points where the system could fail. This boggledness, however, suggests that even I, after all these years, still don't properly conceive of the universe inside a cell.