An unfinished poem of the unrequited

My fantasies are sketchy
like the black-and-white outlines
in a colouring book
Were they be too vivid,
they might jump out
of the pages,
the beasts of reality

I caught a sight of you.
The door slightly ajar, I passed by
a glimpse of you
Pangs and twangs
tugging of heartstrings
vibrations too low to be picked up
by human ears
The frequency of emotions
guttural, deep, and low
that which sends blood coursing,
flooding the vessels,
And the vessels are like cracks
on a broken vessel.

Wordless poems

I remember I wrote a post on a swimming forum sometime ago, something about long-distance swimming. Someone was wondering how long-distance swimmers can endure the lap repetition and stuff like that. I wrote something to this effect: I don't get bored because I got to think, pondering about the problems in school, about unrequited feelings, and incubate wordless poems. The phrase wordless poems occurred to me right then and there and has stuck ever since. Wordless poems. Subconscious jumble. Primordial soup of thought. Aren't we all carrying wordless poems in our heads? That which sometimes has never found its home until we die. Those homeless hermit crabs crawling on the beach bordering the sea of knowledge. Wordless does not mean voiceless. Give it volume, construct meanings out of it, give it a home, give it wings, and let loose.

The flag of ignorance

I heard this somewhere, I think, in a Christian apologist's podcast, arguing about absolute truth:

If everything is relative, then this statement is relative, too.

That stuck with me for the longest time because it is a solid shelter in the wake of Postmodernism.

But no, it's not about Postmodernism. I found that people I talk with (or others in a certain social media) are simply using Relativism because they don't bother to find out, really. 

A friend expressed his astonishment when I was reading a book related to Zen Buddhism:

"But, aren't you a Christian?"
"Yes, but what's wrong with finding out more about other beliefs?"
(Shakes head) "My other Christian friends simply wouldn't do that."

That, I don't understand. How can you defend your own belief if you don't know about others'? Now, I can only attribute that to laziness. Postmodernism is indeed one of those terms that is bloated beyond recognition and no one can offer a succinct definition of it anymore. It's a hand-waving, sweeping-under-the-rug thing. I don't bother to find out, so to cut the conversation short, I shove it to that trashbin of meanings, Postmodernism.

On the other end of the spectrum, there is a striking parallel with God of the Gaps thinking -- I don't understand and God is the totality of what's mysterious, what I don't understand. The danger of this, of course, your God would become smaller and smaller as you understand more, like Santa Claus is becoming less and less real when you are growing up.

Seekers of Truth, don't rally under the flag of ignorance.

A Structural Biologist's Manifesto

"So, what are you studying?" Depending on who is asking, the length of my answer would vary. See, since I go to grad school, quite a number of people are asking me that; and answering 'Biomolecular NMR' would draw some blank stares.

So, go back a little: Chemistry. Ah, my undergrad major, and since my lab uses analytical chemistry technique (i.e. Nuclear Magnetic Resonance) to probe biomolecular structures, this answer is not too far off the mark.

"So why are you in the School of Biology?" Ahem. Here we go again.

So, the slightly longer and my supposed official areas of study: Structural and Computational Biology. I think I shall reintroduce my clockwork analogy here. Imagine a clockwork with all its gears running inside. If one would want to know how exactly the clockwork mechanism work, one would want to take it apart and see the gears; how they are connected together, what are their shapes that fit each other so that the concerted mechanism is running. Now, every living thing is also a machine, a biochemical machinery, that, like a clockwork, consists of tiny, tiny parts that are grinding away and give rise to life as we know it. Ideally we want to map how these biomolecular gears interact with each other (i.e. the interactome). Prior to that we would want to know how these tiny gears look like. The structures of these tiny gears are then what the structural biologist would like to know.

'To know' here, as in all areas of science (or anything, really), should be interpreted philosophically. The usual limit of what a structural biologist want to know goes beyond 'having a visual representation'. Sure, it's nice to know what these biomolecules look like since we normally can't see them with naked eyes. But blobby blobs at crappy resolution (say, 15 Å) doesn't tell much. Like a blurry text on a document for example; it's unreadable. What we would like to know, ideally, is the visual representation at the resolution of individual atoms (i.e. atomistic resolution). The blurry text on your document now gains some sharpness; now you can distinguish individual letters; it's now legible. Often, this is sufficient to establish how it behaves, how it interacts with, say, water molecules, metal ions, drug molecules, or other biomolecules.

To even arrive at this point is an accomplishment (to illustrate, resolving a previously unresolved structure of a big protein and analysing its structure-function relationship may occupy the whole PhD thesis, to give you a sense of scale). Could we do better, you ask? Erm, there's actually some problems -- hitting the philosophical wall, so to speak. Let me explain.

*WARNING: TECHNICAL TERMS AHEAD*

So, there are two common techniques used to probe biomolecular structures. (Oh, when we are talking about biomolecules, we mostly talk about proteins -- the biomachinery mostly comprises them).

The first is X-ray diffraction. It works by interpreting the diffraction pattern of X-ray by electron density of the atoms that make up the biomolecule. Since the atoms are arranged in a particular way for a biomolecule, the diffraction patterns are unique to each biomolecule; and long story short, the X-ray crystallographer would be able to construct back the electron densities of the biomolecule, thus she would able build a model of the biomolecule.

Now, problem #1, for a nice diffraction pattern, you would need repeating units, so you would need crystal of your protein, and crystallising a protein is honestly a PITA. Arising from that, problem #2, you would try a lot of different conditions until you find one that is suitable for crystallisation -- who is to say that that particular condition doesn't affect the structure of your biomolecule? Still arising from problem #1, the protein in say, your body, is in aqueous environment, but in your crystal it is obviously in solid -- problem #3, who is to say that your protein structure is not altered by crystal packing, and problem #4, your final structure would be a static snapshot of the structure frozen in the crystal, while the structure in solution must be a lot more wiggly-diggly -- do you now claim you 'know' the structure? (There, your epistemological wall). Problem #5, most of the atoms comprising a biomolecule -- C, O, N, S, Se, and some metals -- have nice, fat electron densities, but that ubiquitous Hydrogen, the most abundant element in the Universe of things living and non-living, does not. As such, H atoms are not visible in the crystal structure. Problem #6, so are regions of the biomolecule that does not form regular repeating units (most likely because they are floppy).  Problem #7, when you are matching atoms to your electron density map, some are ambiguous (e.g. you can point sidechain A at this orientation, it fits ok, flip sidechain A 180° and it still fit ok, even though on one orientation it's N but the other is O -- since N and O have similar electron densities).

So your typical X-ray structure file would miss its H's and its flexible regions (the termini are usually susceptible); some sidechains may not be at their correct orientation; and there's only one frigging, static frame. Would you now consider you 'know' the structure?

Oh, then there's NMR. The laypeople would be more familiar with MRI (Magnetic Resonance Imaging). Indeed the underlying principle is the same: both exploit the same phenomenon, i.e. nuclear magnetic resonance which arises from nuclear spin (which belongs to the wonderful, you-will-understand-better-if-you-don't-try-to-understand-it world of quantum mechanics (for instance, there's no way to visualise quantum spin)). Long story short, NMR yields a set of restraints. If in X-ray crystallography one needs to fit the biomolecule to the little pockets of electron density, in NMR one needs to fit the molecule to satisfy these restraints. So you would have to know the amino acid sequence of your protein. So then you have a totally linear peptide -- make the peptide explore different conformations to satisfy the restraints, a game of Twister if you will. What you end with would be a set of conformers, which would be ranked according to their energy. Usually the first 20 low-energy conformers are deposited in public domain. The fact that there is a set of conformers, called an ensemble, is important. By aligning the conformers in an ensemble, it's usually clear which region is flexible -- the deviation for that particular region would be more pronounced across the conformers. So an NMR structure would have its H's, all amino acids visible and it's not a static snapshot (cf. X-ray structure). Also, if you do solution NMR, it's may be possible to as close to physiological condition as possible (may not be totally tractable because of limitation in NMR setup itself, e.g. NMR signal at high pH condition decays too fast).

While seemingly answering to all X-ray crystallography's woes, the NMR spectroscopist faces a totally different set of problems. First off #1, NMR is an indirect technique, unlike X-ray diffraction which directly constructs a map of electron densities. So NMR structure doesn't really have a concept of 'resolution', which makes it kind of hard to assess the quality of a structure. So, you have made your protein play a game of Twister to satisfy your restraints, now #2, the quality of restraints -- if I see a flexible region in the ensemble, is it really flexible region, or I didn't apply enough restraints, that's why it's fuzzy? #3, the game of Twister is called restrained molecular dynamics, basically a computer simulation. Of course, it's only possible to incorporate approximations and assumptions, not the whole physical law shebang, into the software. Some of those may not be appropriate and may affect the resulting structure in a significant way. There are some technical obstacles as well, like how the protein of interest needs to be isotopically labelled with NMR-active nuclei (15N, 13C). The final step of reconstructing the structure is tedious both for X-ray crystallography and NMR spectroscopy -- so that adds to the time needed to produce a good 3D representation of a protein. 

So, for the umpteenth time, after successfully determining a structure, the structural biologist should ask, metaphysically, Do I 'know' the structure?

Science, people. 

That's it. Next time I will just reply, "I do Science."  

Delightfully Lost and Human

Onsen, yukata, tatami, futon.

Those are some of the things I knew about Japan. Most of my knowledge about the Japanese language and culture came from my extensive manga reading. You may have friends who faithfully follow scanlations the Shounen Jump Big Three — One Piece, Naruto, Bleach — but the amount I read is much more. For example, to my own astonishment, I have to spend one whole day catching up on my manga reading after a two-week trip to Japan, during which I didn't read manga that much due to the limited screen estate of my puny laptop.

My manga obsession aside, I've learned that I have nuanced knowledge of the Japanese culture that my travel companion, an advanced-level student of Japanese language, does not know. I recalled telling him that in several mangas I read, people enjoy a drink of cold milk after soaking in onsen — I was telling him this when we have just finished our own share of hot spring soaking. So I wandered to the vending machine to verify my own trivia, only to discover other bath-related stuff in the vending machine: shaver, soap, shampoo, a pair of boxers — the latter an interesting finding notwithstanding, there was, to my dismay, no cold milk. However, imagine my delight when I paced to the other hand of the changing room and found, you guess it, a cold-milk vending machine. Needless to say, we teetered gleefully to it and fed it some coins. 

There were other moments like this, when my knowledge of some obscure aspect of the Japanese culture showed. On the other hand, there were also moments when my companion has to rescue me from drowning in the verbal torrent that is Japanese speech. And there we go, two people who have some knowledge in the Japanese culture and language, and somewhat lacking in travelling experience.

--

Where one goes on a journey, is quite inevitable really, that one will sooner or later get lost. In my native language, there is an aphorism that says he who is too shy to ask directions will get lost. My companion, who was keen to apply his Japanese language and finding our own way, was averse to asking. Myself, following wisdom of the ancients and being emboldened by the fact that we were in a land of strangers, would go up to policemen or other young-looking people in businesswear (more likely to speak English), said sumimasen (excuse me) and went straight to a mixture of dumbed-down English and animated, flailing, Tarzan-and-Jane sign language. Fear of getting lost triumphs over introversion.

Towards the end of the trip, we visited the Ghibli museum. There was one sentence in the pamphlet that is decidedly stuck in my mind, namely, I paraphrase: The visitor is encouraged to get themselves lost in this museum. Indeed, if you have seen even one or two Ghibli animations, the brand of the fantastical will soon be impressed upon you; what seems like a normal scene gradations into the magical, the preternatural. True enough, for an establishment that encourages one to get lost inside, the interior of the museum is delightfully confusing so that one would be delightfully lost. Upon entering reception, one would choose to view a short animation à la Ghibli, that would jumpstart a fantastical journey; or, one can choose to view various zoetropes of familiar Ghibli characters. Real time animations are hypnotic; it sucks you in, it transcends to your plane of reality: like Hey, this is not the animations you see on your silver screen, these characters come to life; right here, right now. Only after visiting Ghibli museum, I understood that getting lost is okay; that one should wonder and wander in lostness; bringing out that childlike quality of marvelling in everything, worrying not a farthing about how to get home, because one would be home eventually, for now be hypnotised by the present and seize it, the present and the day.

The writing of Augustine of Hippo was described to be 'digressive'. Although undoubtedly this gives headaches to his translators, the commentator mentions this in the tone not of derision, but of delight, because eventually everything would tie in together and the reader is brought to the home of the argument. Augustine would take his reader to a journey with a lot of detours, just like life, that grand scheme of things, is itself a journey with a lot of detours. (If this is not obvious to  the reader by now, I'm using this digression to justify digressions. Feeling delightfully lost yet?)

--

I read travelling accounts sometimes, and now I understand why there is a whole genre dedicated to travellogues: travels expose you, force you to rethink your assumptions and prejudices, shove a new paradigm down your throat. And if that doesn't wring creative juice out of you, I don't know what will.

I foolishly only recently made the connections between manga and cartoon. During my travel in Japan, I was confronted several times with a nagging feeling. The nagging feeling that the real thing does not hold up to my expectations. We were lucky enough to witness summer festivals, where stalls of food and other amusements were set up in the neighbourhood of nearby temples and shrines. In my mind, it was a magical place — you would go to one wearing yukata, treating yourself to takoyaki, candied apples and a game of goldfish-scooping; you would pray at the shrine and give offering, buying charms and draw fortunes; you would wait until late at night when fireworks like a spontaneous field of blossoms would burst, colouring the night sky. Yes, I did witness some of this, but somehow something was lacking. The first fantasy-shattering thing: the price of takoyaki (and other treats) was exorbitant. Secondly, and this is the major source of that nagging feeling: Real people actually do this? The moment this thought surfaced, I realised that I have been treating the Japanese culture as precisely that: a fantasy. In my own imaginations, it has become glossed over, raised to the ideal. In my mind, the Japanese have become 2-dimensional, cartoon figures of themselves.  Kierkegaard would call it a repetition.

And this brings me to the second big thing I learned from this travel, besides getting delightfully lost; that we are not that different after all. Strip that shiny veneer of culture and language and fancy clothes and we are not that different after all. And of all places, I learn this at onsens.

I had an inkling of this already when I first joined the lifesaving team. We strip down to our swimsuits, which are all Lycra, which are all of similar thinness. Understandably, this would make anyone anxious: your fashionable clothes are not there, your fake mannerism is not there; everyone speaks the same language and passion of swimming while laid bare in the bodies you carry with since birth with all its imperfections and what separates you from other human beings is just a thin layer of Lycra. 

And this is also the onsen philosophy: that every man and woman is forced to shed the onion layers of labels that society and oneself have plastered upon. The onsen etiquette prescribes that, firstly, one takes off all one's clothes in the changing room before entering the bath area. Needless to say, what one should take off is not only his regalia, but also his own social status that is implied by that set of regalia, for in the onsen everyone is his own naked self. Secondly, one should wash oneself clean before soaking in the public bath. What one previously has taken off is not enough, one should go a step further and take off the dust and the grimes; and the implication is quite clear: that wickedness and prejudice should be washed off, too. Only then, one is allowed to soak in the public bath. When one has traded his regalia with a cloth of vulnerability; when one has traded his prejudices and wear a robe of humility and open-mindedness. In From A Distance, Bette Midler sang, "From a distance, you look like my friend", but the onsen philosophy asserts that we should transcend that distance and stand nakedly side-by-side and the verse would go "From up close, we are actually the same, you and I".

--  

I would close with another aphorism from my mother tongue that came to mind: "Where the earth is trodden on, that's where the sky is supported", which is roughly equivalent to "In Rome, do as Romans do". And I think most travellers would come to this same conclusion: That deep down, we are all the same. That deep down, we are all humans. That yes, we tread on different earths and burden different skies, but we stand on the same Earth and hold up the same Heaven.