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.

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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.

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.

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!).

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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!

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.

Hia !

That's a dead water monitor.

Supposedly, the critters are the epitome of lizard intelligence. Intelligence, then, is no barrier to wallowing in slime and muck and filth in search of decaying flesh. The Thais focus on the monitor's latter qualities and ignore its maze-navigating talents; refering to another human as a water monitor is a fairly serious insult, something like calling a Frenchman a cow.

The Thais have a number of terms for the water monitor. The insulting term would be "hia." You hear young Thais working "hia" into nearly every sentence, the same way some Americans would use "fuck."

Hia arai? -> What the fuck is that?

Ai hia! -> Oh fuck!

Suay yang hia -> Fucking beautiful

etc.

Oddly, the last time I visited the Dusit zoo in Bangkok, the monitor exhibit was labeled "hia", in Thai. My Thai friends are surprised at that.

Up to a few years ago, you'd say "tua ngern tua tong" if you wanted to speak of a water monitor in polite company. It translates to something like "body silver body gold." However, there's an attempt to clean "hia" entirely out of the Thai language and replace it with a new term; "woranut." It'll never work; can you imagine an American government agency declaring that "fuck" will be replaced with a new term?

The genus name for the creature is "Varanus", which is quite similar to "woranut", especially when you consider that the Thai language has no "v" sound. Also, though Thai words may begin with an "s" sound, an "s" letter gets a "t" sound when placed at the end of a word. Unfortunately, "Woranoot" (double o's) has long been a popular Thai name for girls. It simply means "beautiful girl." So now we have thousands of Thai women suddenly finding their name associated with the finest example of disgustingness in this part of the world.*

A number of superstitions relate to the creature. You should walk to the right (or is it left? I forgot) around a dead water monitor. About a decade ago a Thai man made the news when he adopted a monitor based on the belief that his son had reincarnated as one; you'd see nightly videos of the father fondling the creature with exquisite care, heaping affection on it.

The monitors are not-so-distantly related to Komodo dragons, the biggest of lizards. They're ubiquitous in this part of the world. Even when you can't see one, you might hear one rustling in the weeds, or slinking away into a shallow, scummy canal.

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*The Thais may be the world's greatest name-changers, though. I'm guessing 50% of Thais change their first name at least once in their lives, making searching for old friends on Facebook a bit more problematic than usual. It's generally the result of a visit to a fortune teller who augurs that one's name is inauspicious, offering a number of choices for replacement. So this problem of suddenly being saddled with a disgusting name can be dealt with relatively easily.

What Tiger Shoulda Said

I know this has been done before, but let me give it a shot:

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I'm here to apologize. I made a huge mistake in my life. Getting married. Or, to be clear, getting married with the stipulation that I'd never offer physical affection to another human for the remainder of my life. What a crock!

Some of you may have heard that mitochondrial Eve and y-chromosome Adam were separated by almost 100,000 years. Now why is that? Without going into the math, it's because men have gotten around over the millenia. Historically, breeding males impregnate about 1.5 women. I've brought copies of Wilder, Mobasher, and Hammer's Genetic Evidence for Unequal Effective Population Sizes of Human Females and Males on the subject, for your perusal. Thoroughly peer-reviewed.

We needn't get all mathematical to see the unnaturallness of marriage, though. You might get wistful looking at the bonding that goes on between a few species of birds. I've got news for you...we're primates. Have some fun and type key words like "bonobo, chimpanzee, sex, mating" on YouTube after the press conference.

Yes, I'm aware of the naturalistic fallacy; being natural doesn't make it right. But quit the pearl-clutching. Some of you doth protest too much, I'd say.

Much has been made of my Buddhist practice. Well folks, the typical Thai Buddhist marriage ceremony says absolutely nothing about lifelong fidelity. And, of course, Thai men are world-famous as philanderers. Thai women are the world's greatest penis decapitators (about 100 per year...can you believe that?), by the way, so let's not pretend that Thai women are particularly tolerant of this behavior. The world is complex. And my wife is Swedish. Anyway, people need to quit projecting their Abrahamic values onto me. That's not my trip.

Come to think of it, doesn't the legal enforcement of monogamy violate the establishment clause? Gotta make a note of that.

Yes, Buddhism teaches balance and honesty, and I've veered off in the direction of an extreme. But it also teaches that jealousy and attachment are to be avoided. It's fair to say I'm a success in those departments. Clearly, my wife has failed here, but with 15 minutes of additional meditation per day, she can work it out.

Greed is also a failing that my wife and I are guilty of. Hey...if I'd conquered that, I wouldn't be speaking to you at this moment, now would I?

Some folks call for me to undergo therapy. Folks, I need therapy the same way you need therapy for not believing in Santa Claus.

Hopefully, I can use my celebrity status to inspire folks to reevaluate the sham that is marriage. 50% of the audience here are, or will be, divorced. Some of you have gotten divorced multiple times, and with each new marriage you felt that this was the last. Are you totally fucking unconscious? Of the remainder, a large portion will find themselves sleeping in separate beds. Or, at least, with one of those long pillow things delineating territories on the bed. Whatever. Let's not be ashamed to greet the new day with arms that are not numb, with fluid shoulder joints, as individuals, unafraid to see a movie alone.

Thank you!

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After writing the above, I googled "What Tiger Should Have Said." Wow...so many tracts with that title! Plenty of good humor, mostly from the "I'm Tiger Woods, and you wish you were" camp. Some racism too...white racism, black racism, nothing unexpected.

But there's also an army of condescending, judgemental Christians bloggers out there, evaluating Tiger's sincerity. He didn't go far enough, of course. His voice was too monotone. Blah, blah, blah. One blogger, an admitted ex-sex-addict minister, tallies up 10 positives and 3 negatives in Tiger's outpouring. For others, the speech didn't dwell enough on all the folks he has hurt, apparently. As far as I'm concerned, there wouldn't be nearly the hurt if Americans would loosen up their expectations of marriage.

Then there's a number of disgusting attempts to degrade Buddhism along the way. As usual, the Christian detractors begin with a straw man and proceed to disassemble it. In this case, it's the Buddhist attitude toward desire. See, us Christians are taught to desire God, but Buddhists are taught to desire nothing. This comes as a surprise to those who are taught that Buddha desired the enlightenment of all sentient beings, or who have taken the Boddhisattva vow.

Science as a Search for the "Mind of God"

Why did science arise in the West? That's a loaded question; plenty of folks would argue that "science" arose elsewhere. Still, a quick scan of your surroundings will reveal electronics, plastics, time-keeping widgets, lighting, senders/receivers, engines, etc. It's Western stuff.

One Steve Fuller has an answer to the question: Christians, inspired by a search for the "mind of god", propelled science forward. Surprise, surprise, this Jesuit-educated disembodied blathering head believes that a Christian philosophical quest is responsible for science.

I find the view ludicrous. As I wrote on scienceblogs:

Let's not consider contingency,accidents, and snowballing effects in the development of science. Forget about climate and geography. Ignore abrahamic religions' needs for evangelizing and warmongering and manifesting/discovering magical substances. Toss out any complicating arguments about abrahamic religions' anti-science propensities. Toss out neutral events too (e.g. a need for time-keeping devices for medieval monks). Ignore what non-abrahamic religions actually say, and poo-poo any science that did emerge in non-abrahamic areas. And then Fuller can claim that science was motivated by the religion of his upbringing.

Fuller also says that the Abrahamic view that humans (as opposed to animals) are privileged, being created in the image of god, was a historical driver of science. Obviously, Hinduism and Buddhism lack this sort of creation myth, but anyone with a slight familiarity with these religions will know that humans have a superior birth to animals. The Tibetans, in their juicy way, compare the souls competing for a privileged birth while two humans are copulating to flies on meat.

Enough of my own views, however. How about the views of the folks around me at Mahidol University?

An Iraqi Student: The era of Muslim domination of science (roughly 900-1300) might have continued indefinitely had the Hulagu Khan not invaded Baghdad in 1255. He says the Tigris River turned blue as ink leached out of the pages of books that were tossed there by Mongol forces.

An Indian Muslim: The Western concept of separation between church and state was responsible for the rise of science in the west over the last 400 years.

An American Ichthyologist: Refuses to cop to the notion that science is a Western development, even when I attempt to narrow the scope down to the last few hundred years.

A Thai Toxinologist: The need for the technologies of war spurred science in the West.

The Director of a Dengue Research Lab: Life is easy in the tropics. Just pick a mango off a tree and gather up some frogs in the forest. Ingenuity was required in cold climates, however. He was also quick to chuckle about the supposed Christian/science link, knowing full well that Christianity has a history of feuding with science.

I'll add more views as they come in.

A few more words of my own: Ask for an example of non-Western ingenuity, and it's a decent bet that you'll get the Chinese invention of explosives. I wonder, though, if systematic thinking, a hallmark of science, was at all responsible here. In the bomb-making case, was there ever any attempt to formulate hypotheses, falsify them, and build on the results? And, if systematic thought is crucial for "real" science, how could the destruction of books signal the end of science in the Middle East? It seems like we need to discriminate between mere "technology" and "science", how-to-manuals and deduction/induction. Maybe my own cultural bias/ignorance is showing here, while I'm griping about someone else's. Correct me, if you wish.

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Oh, the pic above is Marcel Duchamp's "Bride Stripped Bare by her Bachelors, Even." I don't dig it, but it came to mind, somehow.