Tuesday, December 30, 2008

The latest horror story I'm reading is:

"Mosquitoes were selected from the same cohort 6 or 7 days after emergence. For injection, overnight-starved mosquitoes were fed for 20 min directly on a restrained chicken with parasitemia between 15 and 30%."

Saturday, December 27, 2008

Book review, The Dispossessed, by Ursula K Le Guin. First published 1974.

At its heart, The Dispossessed is a delicate tale of relationships. A classic fantasy of a hero protagonist's growing-up years trailing all the way to middle age, the hero spends a great deal of time talking to himself or to no one at all, this being the key relationship in the book. I could have said that this was a tale of despair and impotence in the brilliant hero protagonist, but that would be imputing too much emotion to Le Guin's writing therein. Murakami, she certainly isn't.

In similar detached white kaolin-screen adolescent vein, the hero consistently discovers "essential" and apparently eternal truths about relationships while talking to (and at) near-strangers. Finally, he manages to neither die nor create an international diplomatic incident while escaping the riot he was the symbolic figurehead of. Borne away on a spaceship, deus ex machina style, he would do Superman proud. Interplanetary Zen, here I come.

Is this science fiction? What happened to the science that advances the hero's insight or promotes dramatic development? (Oh, but thank you for the idea of the ansible. That was good for Orson Scott Card later.) A twin-planet system does not a science fiction novel make. There was precious little attempt at each planet mirroring the other, barring the hero protagonist's momentary shock of 'coming home' on first landing on the 'other' planet; the story would work equally well across a mere ocean instead of deep space.

Clearly this book tries to do too many things. Ballerinas look ludicrous doing hip-hop with full ballet technique, and I think Le Guin's thoughtful meandering style in this book does not suit the heavy topics of anarchy, solidarity, capitalism, libertarianism, communism, implications of the Milgram test (the prison experiment, updated as the "Lucifer Effect" by Philip Zimbardo), education, freedom of information, and national sovereignty. I've seen the word "philosophical" being used to describe this book, in Amazon reviews. To paraphrase Alexander McCall Smith (thanks Gabriel), this is political philosophy at the level of a soap opera. There just had to be a violent riot in it somewhere, didn't it? No kidding.

In addition, alternating the hero's past and present between fairly long chapters does the story arc a grave injustice, forbidding the feebleminded reader from walking along Shevek's physical journey and development of thought. When re-reading this book to find some redemptive element in it, I was freshly annoyed by how Le Guin expects the reader to remember half a sentence in Shevek's future that refers to an incident fully explicated in Shevek's past some 70 pages hence. While this chapter alternation could be an attempt to portray the book's science fiction element of the circularity of time and simultaneity of objects, it fails to make Shevek's motivations clear at any step, and is gimmicky.

It did not connect with me on any emotional level, impossibly bland, the reminiscence of a cup of tea made from the last scattered handful of tea leaves in one's cupboard on a long slow afternoon when one feels a compelling buzzing irritation of seeking to do something yet having absolutely nothing else to do for the day. I vastly preferred Le Guin's The Left Hand of Darkness, published in 1969, five years before. Now that is science fiction.

Friday, December 26, 2008

I am back at work tomorrow (technically, today). The thought is strangely ... exhilarating. I think I've gone to too many gatherings where women are expected to be traditionally decorative and unopinionated.

Monday, December 15, 2008

"Ha ha! Of course not!". Thank you. Thank you very much, that is good to hear. I had to ask; some guys are really nuts, and being married is no assurance of "quality control" either. ;)

I heard this on the radio yesterday, while doing my weekly household chores between the lunch and dinner gatherings. It's been a while since a song has been this arresting. And it's a very old song, without sounding like one.

Beautiful girl, wherever you are
I knew when I saw you, you had opened the door
I knew that I'd loved again after a long, long while
I'd loved again

You said "hello" and I turned to go
But something in your eyes left my heart beating so
I just knew that I'd love again after a long, long while
I'd love again

It was destiny's game
For when love finally came on
I rushed in line only to find
That you were gone

Wherever you are, I fear that I might
Have lost you forever like a song in the night
Now that I've loved again after a long, long while
I've loved again

It was destiny's game
For when love finally came on
I rushed in line only to find
That you were gone

Beautiful girl, I'll search on for you
'Til all of your loveliness in my arms come true
You've made me love again
After a long, long while
In love again
And I'm glad that it's you
Hmm, beautiful girl

Perhaps unwittingly primed by this song, I walked into my dinner gathering and was promptly charmed by this very cute guy (so completely my pattern! aiyoh! so cute! *limp-wristed waving*), who, alas, showed no especial interest. The alcohol slowed me down some too.

But during the party I heard from my host -
- one of our mutual friends our age had died.

Indirectly because of something I had failed to do last October. Something that we had all failed to do.

I hope you will find love, wherever you are, Z. Rest in peace, and we will meet again, after a long long while. You were beautiful. I remember you, and I will miss you.

Tuesday, December 02, 2008

SCOP and CATH are the two indispensable structural classification databases for proteins ("Look, Mummy, my nose looks like yours!" "Yes I see that too dear, the curve is short and sharp." "But it's also short and sharp quite like your friend Aunty Maria's....."). However their respective introductions leave a lot to be desired.

The following are taken from a textbook by Arthur Lesk, Introduction to Protein Architecture (OUP 2001), which I've quoted from before. Page numbers are indicated. Underlined words are my emphasis.

SCOP (pg 127-128)

SCOP organizes protein structures in a hierarchy according to evolutionary origin and structural similarity. It is based on protein domains rather than full protein structures. At the lowest level of the SCOP hierarchy, then, are the individual domains, extracted from the Protein Data Bank entries. Sets of domains are grouped into families of homologues. These comprise domains for which the similarities in structure, function and sequence imply a common evolutionary origin. Families that share common structure and function, but lack adequate sequence similarity, so that the evidence for evolutionary relationship is suggestive but not compelling, are grouped into superfamilies. Superfamilies that share a common folding topology, for at least a large central portion of the structure, are grouped as folds. Finally, each fold group falls into one of the general classes. The major classes in SCOP are Alpha, Alpha + Beta, Alpha / Beta, and 'small proteins', which often have little secondary structure and are held together by disulphide bridges or ligands (for instance, wheat-germ agglutinin).

CATH (pg 129)

CATH presents a classification scheme similar to that of SCOP. The letters in its name stand for the levels of its hierarchy: Class, Architecture, Topology, Homologous superfamily. In the CATH classification, proteins with very similar structures, sequences and functions are grouped into sequence families. A homologous superfamily contains proteins for which there is evidence of common ancestry, based on similarity of sequence and structure. A topology or fold family comprises sets of homologous superfamilies that share the spatial arrangement and connectivity of helices and strands of sheet. In CATH, architectures are groups of proteins with similar arrangements of helices and sheets, but with different connectivity. For instance, different four alpha-helix bundles with different connectivities would share the same architecture but not the same topology in CATH. Finally, the general classes of architectures in CATH are: Alpha, Beta, Alpha-Beta (subsuming Alpha + Beta and Alpha / Beta), and domains of low secondary structure content.

The correspondence between the levels of the hierarchy in SCOP and CATH is rough but not exact.

SCOP class = CATH class
SCOP fold = CATH architecture, topology, homologous superfamily
SCOP superfamily
SCOP family = CATH sequence family
SCOP domain = CATH domain

A comparison (pg 131-132)

Do the different classification schemes agree? Recognize that to classify protein structures (or any other set of objects) you need to be able to measure the similarities among them. The measure of similarity induces a tree-like representation of the relationships. CATH, SCOP, DALI and the others, agree, for the most part, on what is similar, and the tree structures of their classifications are also similar. However, what an objective measure of similarity does not specify is how to define the categories that you call the different levels of the hierarchy. These are interpretative decisions, and any apparent differences in the names and distinctions between the levels only disguise the underlying general agreement about what is similar and what is different.

Monday, December 01, 2008

A Russian-American teacher speaks about how education is necessarily to achieve competence in something and contrasts his learning under communist Russia with that in American undergraduate education. Published 1993 (pdf).

Link courtesy of Jiahao.

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