Science through a blind eye

Full article here.

Excerpts:

When Forest met Cordes in 1998, she was new to the faculty and had hardly worked with graduate students, much less a blind one. But she saw no reason Cordes could not contribute to her team. For one thing, he was a computer whiz who had written code since he was 10. Forest initially figured he would dive into the mountain of data created by crystallography trials and help resolve the structures of the bacterial proteins her lab was studying. But when that task was completed, “ Tim’s project evolved in a different way,” says Forest. “He ended up doing a lot of lab work, which I wouldn’t have expected to be right up his alley.”

...

TimMol’s alternative concept is quite simple. It replaces the three spatial dimensions with three different kinds of audio cues, so that atoms inside a protein become like speakers in a surround-sound system. From a given point inside a protein, a user can hear what other atoms are nearby, placing them by the pitch and orientation of the sounds they make. A higher or lower pitch indicates that the atom is above or below the user’s position. Louder means closer, while softer means farther away. Atoms to the left play in the left ear of the user’s headphones, and those to the right play in the right. To help distinguish different kinds of atoms, Cordes assigned each a musical instrument—piano for carbon, organ for oxygen. “I picked kind of a cool, jazzy vibraphone for nitrogen,” he says, “ because nitrogen is usually shown in blue in models.”

Partly for amusement, Cordes included a function that plays an entire protein by tracing its backbone of amino acids, creating a meandering trail of rising and falling notes. It sounds like some kind of minimalist sonata, but the tune is deep with significance. “Usually, when I come to a new protein, one of the first things I do is to play it atom by atom,” Cordes says. “It helps you get an overall sense of what you’re looking at, and you can get a feel for its shape and structure.”

My reaction to this is not so much "wow amazing a blind biochemist" as "good grief this guy is a bloody genius".

Oddest titles

Mary Schneider's column - reporting on the Diagram Prize for Oddest Title.

The sad thing is that "Proceedings of the Second International Workshop on Nude Mice" makes perfect sense to me.

Vitamin A study

This is SOFA KING ironic. I can't participate in a nutrition study that would provide me with free food because I don't weigh enough.

I'm sorry to say that I can't enroll you in my study because you are too lean! I really appreciate your interest and time.

Thanks,
Ashley
....
....
Tanumihardjo Lab
Department of Nutritional Sciences

Anyway, the point of this study is that the researchers want to look at Vitamin A levels in young, nonpregnant women because they "believe the intake recommendation may be too high".

The study is going to provide participants with groceries for twelve weeks. Deviations from the provided food must be logged, and they definitely aren't allowed to eat anything on a list of Vitamin A-rich foods. (I was happy to see that garlic wasn't one of them...my diet scares vampires.) I spend about $160 per month on groceries...I do eat a lot for a girl and I prefer fresh food, or at least dishes that have SOME fresh ingredients rather than frozen or all-instant meals. I'm not in great shape financially, so the free groceries sounded great on that front even if the menu wasn't all the stuff I like.

I had to fill out a long questionnaire on my eating habits plus the typical short "are you asthmatic/anorexic/alcoholic" health questionnaire. Then I got to sit inside this peculiar chamber called a BodPod that measures body composition...but it makes you feel like an astronaut. (Yes, that's a real picture from the manufacturer and not a starship's lifeboat from a 70s science fiction show.)

Unfortunately, not only am I underweight according to the NIH's body mass index scale, the percentage of fat in my body falls under "Ultra Lean[Women]: 15-18%: Fat levels sometimes found in elite athletes."

WHATTTTT????

I like to go for walks in the woods with my cat. I like cycling with the wind at my back on a sunny day. I like capoeira when I can get over feeling intimidated by the instructors. I swear it's gotta be genetic. My 60+ year-old aunt who's had 2 kids has dresses I can't fit into.

*Looks at bum* There's a little bit of cellulite there! Come on! *pinchpinch jiggle jiggle* The "elite athletes" thing make more sense if I was my sister who's been running cross-country for the last 15 years. It would be more funny if it didn't mean missing out on 3 months of free food...sigh.

Another little irony is that Ms. Valentine told me she's too skinny to qualify as a participant in her own study. Well, if anyone else at Madison reads this, you could try looking up the lab that's conducting the study.

Yes, I just wrote an essay complaining about being too skinny...I'm sure a lot of girls would want to kill me. I just wish I wasn't so blasted hungry all the time *putters off to find midnight snack*

Immuno in space

I love how the authors of this paper are looking to the future:

The development of T cells in newborns and young adults living in the microgravity environments of space or on other planets may therefore be compromised, leaving these individuals susceptible to infectious diseases due to their inability to develop a fully functional immune system.

Woods CC, Banks KE, Gruener R, DeLuca D. Loss of T cell precursors after spaceflight and exposure to vector-averaged gravity. FASEB J. 2003 Aug;17(11):1526-8. Epub 2003 Jun 3.

So...we no can has babeez on spaceshuttle. Yet.

But I really hate journals that force paper authors to stuff all their figures at the end. Figures should be put as close as possible to the relevant text so you don't spend half your reading time flipping back and forth trying to see what goes with what - major pet peeve.

(almost) 3-month update

It's been nearly 3 months and I'm on track for keeping my weird New Year's resolution so far.

Total amount of money spent on clothing, entertainment, stationery and art supplies, bike supplies, and eating out: $377.54.

Total donated to church, Fistula Foundation, Doctors Without Borders, and World Vision: $403.50.

I'm not trying to brag about being a generous person but I'm trying to make the point that even on a relatively small wage like a grad student stipend (my monthly take-home salary is slightly above $1100), you do not need all of that money. It's entirely possible to spend as much on helping other people as you spend on keeping yourself happy.

When I hear people complaining about being "poor college students", I want to give them "a tight slap", as Malaysians say. Except in a very few cases, if you're in college you are by definition not poor. Even if your family is poor, probably you're getting a scholarship equivalent to tens of thousands of dollars per year. Being able to attend university, and especially graduate school, is a huge privilege that's only available to a small fraction of the world, and if I hear you complaining that it makes you "poor" I WILL SMACK YOU.

(hmm...if you look in the sidebar on the World Vision donation page, the pie chart showing expenditures shows that their overhead is 14% of revenue now. It's gone down since the last time I looked. In a world where Christian organizations are often accused of being profiteering and corrupt - sometimes correctly - it's good to see good stewardship.)

I love Microsoft Money because I tend to be disorganized...before I started keeping accounts, the $ would disappear and I'd wonder where it went because I didn't think I spent frivolously often. Turns out the little things add up.

Also, MS Money revealed that I eat A LOT of food...around $160 a month or so in groceries, that's $40 a week. And it's not like I'm some kind of fancy gourmet...I'm just HUNGRY and I like fresh veg.

Lina's upkeep is really cheap so I'm waiting for it to build up before I find an animal welfare wildlife conservation organization to give "her" share to.

Recursive blooper

I thought the BBspot website was malfunctioning when it coughed up a BBlooper that I'd submitted months ago. No...it's a blooper within a blooper (see the sidebar ad in the picture).

Shabery to hear out bloggers

I'm re-posting this article from The Star in its entirety because Shabery is astounding in his clarity, after years of government Ministers and UMNOputras calling Malaysian bloggers seditious idiots (how any group can be a bunch of "housewives" as well as a major threat to national security at the same time is beyond me.)

KUALA LUMPUR: The Government will not control bloggers but will consider their views as well. That is the assurance given by newly-appointed Information Minister Datuk Ahmad Shabery Cheek, who is planning a meeting with the blogging community “in the next few weeks to hear them out”.

“The alternative media, like bloggers, play a role in nation building. It is the most direct and simple channel for people to voice their opinions. Sometimes, they can bring about a negative effect but it is mostly positive.”

Shabery said some had overlooked the significance played by bloggers, who could now form their own personal broadcast centres via their websites.

He dismissed the view that bloggers sided with the Opposition, saying that the bloggers only expressed their personal opinion.

“Bloggers are individuals and they have differing opinions. I cannot say that they are all Opposition. Sometimes, they are seen to support the Opposition but sometimes they criticise the Opposition too,” he said.

On whether the Government would enforce some control on the blogging community, Shabery said they would not do so.

“The question of controlling bloggers does not arise. As the saying goes, you can lead a horse to water but you can't make it drink,” he said.

Asked if there was a message that he would pass to the bloggers in the meeting, Shabery said: “It is better that I be a listener first”.

To a question whether the mainstream media had lost its credibility and relevance due to laws governing the media, he said that the rise of blogs was a global trend, adding that this, however, did not mean that people had sidelined the media.

“No matter how free the mainstream media is (from government control), like in the USA, UK and Australia, it is still subject to the standpoint of their respective media (organisation) heads. So, people will still seek alternative news,” he said.

Modded vs. Mainstream

I've gotten sort of addicted to reading BMEzine (Body Modification Ezine) over the last couple of years, since before I got my first tattoo (first and only so far; definitely more to come). Since it's an alternative lifestyle site, you'd expect people to be quite liberal - and I mean in the broad sense, not the abusing-English-languge-US-political sense - but there are some people on there who are quite as fanatically anti-mainstream as some "normal" people are bigoted.

Check out the comments section of the post linked to in the conversation below. Don't scroll up to the pictures if you're at work. Just know there's a mostly naked woman with piercings in interesting places and augmented breasts.

[22:42] me: *groan* people on ModBlog are stupid
[22:42] Steve: ?
[22:42] me: OK...people in an online community DEDICATED to implanting strange things in your body are bashing fake boobs
[22:42] Steve: ...
[22:42] Steve: ROFL
[22:42] Steve: why?
[22:42] Steve: cause it's too mainstream?
[22:44] me: they're coming up with all kidns of wanky arguments like “There are some well documented differences between cosmetic surgery and non vanity-based modifications. The main differences are the motivations behind such actions and the outcomes of each."
[22:44] Steve: why are they angry? how are they not happy with it?
[22:44] me: but frankly those are after-the-fact arguments. I'm pretty sure the people who are sneering at fake boobs it's because they're too mainstream.
[22:44] Steve: ahh
[22:44] me: here...*sigh* look at poster #16. he's quoting from some other forum. http://modblog.bmezine.com/2008/03/17/nipple-shields/#comments
[22:45] me: don't scroll up though, the pictures are NSFB (Not Safe For Ben)
[22:45] Steve: that's a bit nsfbigben
[22:45] Steve: rofl
[22:45] me: LOL
[22:45] Steve: wow
[22:45] Steve: thinking way too much alike

(Ben is Steve's extremely conservative friend whom he's visiting for spring break.)

Liang Hui Fang, d. 2008

My other grandmother was cremated today. She passed away on the 13th, after having been in and out of the hospital for a week due to respiratory problems.

Maybe I'm a bad person but I don't feel sad about her...first because I never was emotionally close to either grandmother, second because she had a relatively long and healthy life (except for Alzheimer's in the last decade). I don't support human euthanasia, but when you're that old and not in shape to enjoy life any more...leaving it's not bad.

It's for my father, aunties, and uncles whom I'm sad for. Especially for my dad's youngest sister, who's single and lived with her mother for decades. (wonder...if i was her would i feel desolate or relieved? am i a horrible person for even thinking that?) This can't be easy on my mum either, as she just lost her own mother in December.

You see, we're not sentimental people. When I got the email from my aunt I called my mum's handphone, since my dad was doing the driving from to KL from Penang.
"How's Pa?" I asked my mother.
"Pa's okay, he's not crying unless you ask him to talk about Maa Maa."

Later when they got to PJ I called my dad's handphone again.
"So how's everybody now?"
"We're all right...I think the only two people who are crying are Tini [the maid who was hired to take care of my grandmother] and your sister [my second sis, who tends to be more emotional]."

So the funeral was today and I haven't heard a report yet since I forgot to call in the morning. My first sister and my brother came up from school on the weekend and took the midnight bus back to Singapore after.

But, oh god,
Under the weight of life,
Things seem brighter on the other side...
Lighter on the other side...

- Dave Matthews Band, "Big Eyed Fish"

So why's HE still...?

Reading news from home is like having a face full of pimples. You can't help wanting to pick at it:

NEP is no more ... it's the NDP lah!

KOTA KINABALU: Sabah Progressive Party president Datuk Yong Teck Lee is puzzled why there is so much fuss over the New Economic Policy when it has already been superseded by the National Development Policy.

He questioned why politicians on both sides of the political divide, in Penang particularly, were still harping in the issue of the NEP that had expired in the 1990s and replaced with the NDP.
...
“The successor to the NEP was the NDP,” he said, adding that overtime Vision 2020, 10-year Outline Perspective Plan (OPP), five-year Malaysia Plans and other policies overshadowed the NDP.

“We are now busy with other new concepts like development corridors, Agenda Baru (New Agenda) and Islam Hadhari (Civilisational Islam). It is no wonder that some politicians both from ruling and opposition have lost focus on which policy to talk about,” he added.

He said the DAP-led Penang government “so-called cancellation of the NEP” was completely redundant because it no longer existed and it was disappointing that Penang Umno was still harping on the NEP like it was a valid document.

Well, maybe they're still harping on it because from what we've seen over the last decade, "NDP" is an abbreviation for "more of the same old crap". Even many Malays, who are supposed to benefit from it, weren't happy this time around.

Besides, we have leadership from the top!

Pak Lah: Most policies are federal policies

PETALING JAYA: Almost all of Malaysia's policies, including the New Economic Policy (NEP), are federal policies, said the Prime Minister.

AAB must have been sleeping when the NEP was abolished.

From Bumiputera Malaysia.
From Kickdefella ("kick the fellow"), more great movie parody posters here. I think my favourite is the "Dah Benci Kot".

Iki Piki's splanch

EDIT: Just realized that if I'd read all the way to the bottom, my scenario (b) is the same as described by the last bullet-point list on the page. One splanch, travelling back in time twice, resulting in a period of time where the same splanch exists in three different locations.

David Morgan-Mar is an Australian physicist who does a comic called Irregular Webcomic, with good reason. The graphics are mostly done by taking photos of Lego minifigs or tabletop game miniatures. It's updated more or less daily, which makes it one of the most regular webcomics in terms of timing. The "irregular" bits are his truly loopy sense of humour and the several totally unrelated storylines alternating with one another at will.

One of the storylines involves a couple of incompetents called Iki Piki and Serron, gambling on sports, and illegal organ trafficking. At this point it's so mixed up that the transmigrations of their organs have become a talking point on the IW forums. Click here and scroll down for the discussion.

The issue that's being discussed goes sort of like this:

1. Iki Piki and Serron end up in jail and have their organs forcibly removed.
2. While in jail, they meet their future selves who have travelled back in time, and these future selves also have their organs removed.
3. The "first" IP & S are dumped in an alleyway to die, but they find a set of organs that conveniently match their species and blood types in a suitcase.
4. Later Iki Piki steals a second set of organs, so now they have extras.
5. They travel back in time...goto 2.
6. They now have one set since they acquired the extras at step 4.

The discussion center around how you get THREE sets of organs in the jail cell at step 2, while there are only two sets of Iki Pikis and Serrons. Several people assumed that organs were going around in an infinite loop.

I think I've got it. You either have
a) one splanch that was "born" with Iki Piki and travels back in time ONCE, and another splanch that exists in a closed loop which probably wouldn't work since the organs would become infinitely old; or
b) one splanch that travels back in time TWICE.

You get b) if the set of organs that's removed from the future Iki Piki and Serron are the ones that were originally removed from the earlier Iki Piki and Serron. The future-IP&S-who-traveled-back retain a set of organs that has traveled back twice, removing these from further loops.

If the set of organs that they RETAIN are the original set, the other set which is retrieved and removed must be floating around forever.

Order of organ retrieval (i.e. which one is the set they find in the alley which saves them from death, or the "extras" IP steals later) does not matter.

And why am I analysing webcomics past 1 am...

Five states!

Kelantan, Penang, Perak, Selangor, and Kedah! *happy kitty dance*

I'm sorry to say this about a newspaper where one of my favourite aunties is a journalist but...The Star needs to stop licking the boots of losers. I was once told that The Star editors would hang up pro-MCA banners in the offices during election but thought it was an urban legend until I saw their awful, AWFUL coverage of this year's... Hehe.

Transmission of information

This is a perfect example of how influential the USA is, that even a roadside hawker in Kelantan (the only state in Malaysia that is was controlled by an Opposition party before yesterday's election) knows who one of the presidential candidates is. Probably the owners of most small mom-'n'-pop restaurants here don't even know there's a country called Malaysia let alone that we're having elections in the same year as them:

“Yang kito nak kat Malaysia ni pemimpin yang bermutu, buke pemimpin yang penipu! Kok Amerika tu ado Barack Obama, yang Negro tu. Hei, baik pun Negro dio tu, dio tu orgre bermutu, bukan mace Bush yang buat cerito gilo di Irak. Nah, pemimpin begitu loh yang kito nak di Malaysia ni”

(Rice stall owner, in front of Muhammadi mosque, Kota Bharu)

It's from an article titled "Vox Pop ala' Kelate" on Malaysia Today. Kelantanese speak a unique dialect of Malay...it's quite different to listen to. One of my favourite musicians, Zainal Abidin, uses it in some of his songs.

Anyway, translated:

What we want in Malaysia is quality leaders, not leaders who are liars! In American they have Barack Obama, that Negro guy. Hey, even if he's a Negro he's still good, not like Bush who's doing crazy stuff in Iraq. There, it's leaders like that we want here in Malaysia.

(NB black people are still an unusual sight in Malaysia, outside of the urban areas where there are a fair number of African college students.)

Waiting

So...waiting for final election results. BN lost its 2/3 majority so they can't screw around with the Constitution any more. w00t!

Also, waiting for somebody to go...last week my aunty wrote an email saying that it looked like my father's mother was about to pass away (mum's mother went in December). Since then, the family members have been visiting her, making preparations, et cetera.

I just got an email with what's essentially the brief minutes of a family meeting wherein is outlined the plans for her funeral. It seems very odd to me...there haven't been many deaths in the family in my lifetime, so I always think of funerals as events hastily organized, under emergency circumstances.

I'm young and I feel, to use a cliche, immortal... It seems weird to think that death can appproach so slowly you can see it from a long way off.

Green power

Hoho, sweet. My electric company's trying to persuade customers to pay a bit extra to switch to renewable power sources; apparently I use so little that the extra for me will be almost nothing. Yay!

Only one choice?

Saw this full-page ad in Friday's theSun (obviously, I'm reading the electronic version, but the website has PDFs of the newspaper pages).

I've got news for you, Barisan politicians: the only countries where the people have "only one choice" are TOTALITARIAN FASCIST states.

PowerPhluff

There's something remarkably perverse about taking study breaks from composing a PowerPoint presentation of a paper, to read a book where the author tells you how PowerPoint makes presenters stupid, holds audiences captive, sucks for technical data in general, and was responsible in part for the deaths of 7 astronauts on the Columbia shuttle.

I'm not kidding. Read Edward Tufte's Beautiful Evidence. It's a great book, spurring me to think about what I'll need to do to best present my work in the future, and its publication is responsible for the resurrection of Minard's map of Napoleon's Russia campaign that's being bandied around by the mass media. But I think it's sort of funny that he hates PowerPoint so much that he devoted an entire chapter to it, but I can see his - 'scuse me - points very well. I've had some professors who, when their laptop won't talk to the projector, can't flipping remember what that big whiteboard hiding behind the screen is for.

Minard's map:

Potato boy

From bash.org:

#151227 +(8019)- [X]

IronChef Foicite: well, there's a lot of reasons
IronChef Foicite: i mean, roses only last like a couple weeks
IronChef Foicite: and that's if you leave them in water
IronChef Foicite: and they really only exist to be pretty
IronChef Foicite: so that's like saying
IronChef Foicite: "my love for you is transitory and based solely on your appearance"
IronChef Foicite: but a potato!
IronChef Foicite: potatos last for fucking ever, man
IronChef Foicite: in fact, not only will they not rot, they actually grow shit even if you just leave them in the sack
IronChef Foicite: that part alone makes it a good symbol
IronChef Foicite: but there's more!
IronChef Foicite: there are so many ways to enjoy a potato! you can even make a battery with it!
IronChef Foicite: and that's like saying "i have many ways in which I show my love for you"
IronChef Foicite: and potatos may be ugly, but they're still awesome
IronChef Foicite: so that's like saying "it doesn't matter at all what you look like, I'll still love you"

Steven is my potato.

I bet it's going to be a week before he reads this.

Barisan Rakyat

I really like the Barisan Rakyat poster. I think it's well-balanced in terms of colour and lines...composition is overall nice and I like the font, but it's a bit the weird that the second "RAKYAT" is glued to the top of the picture.

I'm planning to print it out big and attach it to my backpack so people will see it as I walk around...there are quite a few Malaysian students in town (especially undergrads on Public Service Department scholarships haha), so SOMEbody will know. Click for big size: