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.

A Conversation with Mr. Oarfish

As a kid, I had a collection of flashcards with pics of fish on one side, and their specs on the other. The oarfish stood out as the weirdest and most captivating of the lot.

One of the folks I bump into fairly regularly at the Institute is an ichthyologist...a fish expert. Over lunch, I asked him if he had seen the recent video of an oarfish in deep waters:



I expected my acquaintance to express surprise that such a video existed. Instead, I got a 30 minute lecture on the subject of oarfish. It turns out he might be the single most oarfish-knowledgeable individual on the planet. He didn't seem thrilled about the possibility that I'd blog on his knowledge, possibly because some of his opinions haven't been thoroughly vetted by the science community, so I won't offer his name. But here's what I recall:

The video shows the oarfish in a vertical position. Mr. Oarfish expressed skepticism that the fish, Regalecus, actually spends sizeable amounts of time in that position; it might be reacting to the unmanned submersible taking the video or to its environs (which include the massive vertical risers of an oil rig). At the same time, he theorizes that the oarfish may drift vertically in a catatonic state for thousands of kilometers.

I had read that the video was special because previous footage of Regalecus had been taken near the ocean surface; in such a state, the creature would tend to be near death. Mr. Oarfish replied that there's no reason to believe that healthy oarfish don't spend sizeable periods of time near the surface.

Perhaps the single most famous oarfish shot is the following:



The pic is well-known in Thailand. The Thais seem to think we're looking at Vietnam vets somewhere along the Mekong. This notion ties in nicely with the belief that dragons, the Phaya Nak, abide in the Mekong. Mr. Oarfish points out that the uniforms aren't from the Vietnam era. The pic was taken in 1996 near San Diego.

What's more, I had heard the soldiers dined on the serpent following the photo shoot. No, says Mr. Oarfish, the fish was far too decomposed. In fact, he only knows one person who has tasted Regalecus, and that individual was none too impressed with the result. A lousy cook, perhaps.

Some of the maximal lengths are exaggerated. Anything over 8 meters is suspect. An oarfish can actually lose or shed large chunks of its distal region, gecko-like. The resulting sawed-off appearance might lead one to extrapolate wrongly.

Strictly speaking, the species we're talking about here is Regalecus Glesne (Glesne being a town in Sweden). But Mr. Oarfish says there is certainly more than one species that is commonly labeled R. Glesne; there were some fairly large differences in mitochondrial DNA sequences (around 12%) taken from oarfish in Japan and in the Atlantic. What's more, there are significant morphological differences (e.g. in the number of vertebrae).

The evolutionary history of the creature is somewhat murky. One partial fossil from Italy exists, dating back about 1.5 million years...not long enough to display clearcut trends in evolution.

A couple final tidbits...dogs seen oddly attracted to the scent of the fish. And...there's very little evidence of the sorts of predators the oarfish may have to deal with. Sharkbites are rarely, if ever, seen on the creature.

GT200 Update

For some background, here's my first post on the GT200. Following up...

The Science Ministry here in Thailand has conducted tests on the widget. It failed. It seems that extreme caution was followed in minimizing loss of face (sia na), red faces (na daeng), stepped-on-shoes, and so on. Phase I of this delicate operation consisted of banning the public and press from the actual tests.

Face-saving phase II consisted of some twisty phrasing on the part of the prime minister. He said the device "detected" concealed C4 in only 4 of 20 tests, for a 25% success rate. Ignoring the PM's cruddy math, if this $30,000 dowsing rod performed no better than random chance, it can't be said to have "detected" anything. As us farangs say, even a broken watch is perfectly accurate twice per day.

The PM also says that existing GT200s will have to be used in conjunction with other devices, again avoiding hurting the feelings of sensitive generals.

One can really sense the divide between scientists and politicians here. Most of my compadres would like to see all the culprits investigated and outed, with the failure of superstition on vivid display, an opportunity for public education properly exploited. On the other hand, I imagine the politicians saying, "Look, we've canceled future purchases, now it's time for you guys to shut up and go back to your labs." I've no doubt as to who would win this little battle.

Pseudo-scientist Pornthip, mentioned in my original blog on the subject, offered the following piece of warped logic upon learning of the GT200's failure: ""I know it's not scientific equipment, but forensic scientists can use it effectively."

Through the entire hoopla, not a single company rep appeared in the media to defend the GT200. It's funny how a company with such amazing salespeople can have such lousy post-sale support, isn't it?

By the way, there are perfectly legit bomb detection devices out there. They're hugely expensive, require real training, electricity, and upkeep, and can't detect all bad substances known to humanity at a distance of four kilometers. They work, however:

Note: I'm not sure of the source of the Harry Potter image. It's the sort of thing that amplifies quickly via mass e-mailing amongst Thais.

Bad Branding?

Dowsing Hits Thailand

Yikes! The Thai military has purchased at least 500, and as many as 2,000, of these widgets at better than $30,000 each. Do the math. According to the brochure, they detect just about any bad stuff you can name...bombs, drugs, ivory, currency, whatever. "Poppy, cocoa, and marijuana planting areas." Detecting chocolate is nice, but what about coca, from which cocaine is derived? No mention. Hmmmmm. Distance is not an issue..."any thickness of wall can be penetrated, whether concrete, metal, brick or lead." No batteries too!

Similar devices have been used in Iraq, apparently. I'm guessing locales like Iraq and Thailand are good targets for the woo-meisters. Thailand is a world leader in woo, but dowsing has no tradition here; the device looks and feels like any other high-tech mystery box from the West, and few are aware of dowsing's very questionable history.

It was disappointing to see Thai media-darling/forensic scientist Khunying Pornthip defending the device. She gets trotted out every time there's a high-profile murder here in Thailand. Ask a Thai to play word association with her name, and the result is inevitable: "big hair."

I had assumed she was perfectly competent in her craft, but after her assessment of the glorified dowsing rod (well, it's not 100% accurate, it needs to be operated by someone in good physical condition, blah, blah, blah), I now have doubts. Having used the divining rod in the past as a means of detecting bomb residues on corpses, it seems she is now forced to defend its viability or risk humiliation and the wrath of victims' relatives. The military pu-yais ("big people") who ordered the device are in a similar predicament. If they actually recognize the error of their ways, one shouldn't expect a public retraction, but a quiet discontinuation of usage of the "GT-200."

At least in the case of the military, corruption is a reasonable assumption. Let's be generous to the generals, however, and give them the benefit of the doubt. How then, could numerous public figures claim that they've used and validated the device to their own satisfaction? Well, Buddhists (better than 90% of the Thai populace) are familiar with the power of the mind, but sometimes forget that its greatest power may be in its capacity for self-deceit. Witness a gaggle of dowsers exuding supreme confidence in their talents in a double-blinded test, performing no better than chance, and offering up the usual rationalizations (sun spots!) for their failures. It's a five part series, and highly entertaining:

Finally, here's a wonderful BBC expose of a near-identical widget. The company owner doesn't even deny that the ADE651 is, essentially, a dowsing rod.

In all seriousness, it's likely that lives are being lost over this dressed-up medieval artifact.

More on the travesty of the GT-200 here and here and here. It's no surprise to find that the purveyors of this scam have interesting relationships with the law, with the same concept reincarnating under a new name (e.g. "the MOLE", the ADE651, etc.) after the authorities clamp down.

Creating an Auspicious Environment for Biochemical Research

This is the 12th floor of the "Adulyadejwikrom" Building at Sirirat Hospital in Bangkok. Serious research is conducted here in the areas of dengue, thallasemia, and other maladies, making this scene a bit incongruous from my perspective.

Make no mistake, the goal here is to increase the level of good luck in the research facilities for the next year. The ceremony ends with the abbot touring the lab, sprinkling holy water on everyone and everything.

I gently questioned the lab director who organized the affair. Isn't this mix of science and superstition a tad odd? I didn't get a satisfactory answer, though he points out he's also organizing a weeklong meditation retreat that will be entirely devoid of superstition. He refers to meditation as a science of the self. I don't have a big problem with that, though I'm aware of various objections (e.g. in what sense are your "research" findings reproducible/falsifiable?) and would be interested to hear Acharn Pa-Thai's responses.

In fairness, if superstition is ever warranted in a science lab, this might be the place. Floors 3-6 of the building are a morgue. Students report seeing ghosts on the elevator. And floor 2 is a museum where, amongst pickled fetuses, you find the mummified remains of "See Uey", the legendary, cannibalistic, liver-eating, psycho-killer of 1940's Thailand.

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.