Epiphany

Papa had TB when he was a small boy. He was sick for a long time. They gave him streptomycin but it made him deaf in one ear.

Pa's secretary Mr. Roberts has a twisted foot that stands on its toes all the time, because that leg is shorter than the other. He had polio when he was small.

I am scared. They're taking us all out of class when there isn't a different class on the timetable. I am in Standard One and still don't feel comfortable in school, in this cage of dark blue pinafore, grey cement floor and wooden desks, trapped by my lack of language.

Teacher is taking us to the hall but instead of lining up two-by-two as we do for assemblies, we're lining up single file. I can hear girls crying.

There are people in all white who look like nurses. There is a needle in my arm that brings sharp, burning pain. I am told to open my mouth and given a drop of bittersweet liquid.

The taste of the liquid triggers a revelation: I know what it is. We have a book at home that has pictures of sick people. It tells you about all kinds of diseases and how to stop them. There is a picture of a boy who has polio with a twisted leg like Mr. Roberts, and a picture of a child taking a drop of liquid in his mouth.

And I think I'm the only kid in this whole class who knows: This needle and this drop are the magic potion of freedom.

---

And that's how I became interested in vaccines at age six. It just took me 17 years to realize.

That which bends up

Saturday September 20, 2008

26 more Chikungunya cases reported in the country, says Health Ministry

KUALA LUMPUR: A total of 150 Chikungunya cases were reported in the country between Sept 7 and 13, an increase of 26 cases from the previous week.

...

So far, the cumulative number of cases reported nationwide are 1,975 with most of them in Johor (1,098), followed by Malacca (471), Perak (193), Negri Sembilan (124), 40 each in Selangor and Pahang, four each in Kelantan and Putrajaya, Sarawak (two) and one each in Penang and Kuala Lumpur.

The disease is spread through Aedes mosquito bites.

...

— Bernama

The average person reading this will think "OK, 26 people demam. Big deal."

To infectious disease researchers, this is damn bloody scary. Chikungunya is an emerging disease in SEA (originally from Africa). There were virtually no cases last year, but now there have been 1098 in Johor alone, 1975 nationwide total.

It's spread through Aedes mosquitoes, which helps (the virus, not us) since it's an animal vector that is already quite plentiful in M'sia.

I'm getting increasingly fed up with science reporting in the mainstream media. This ought to be in BIG RED LETTERS on the front page. Something like EXPLODING AFRICAN VIRUS CRIPPLES THOUSANDS OF MALAYSIANS. Then maybe there would be some decent funding and infrastructure for biotech research.

Lots of "tampon"

I found a Western blot protocol on our French postdoc's bench in which the word "tampon" appears a lot. Naturally intrigued, I looked at it for a minute and came to the conclusion that "tampon" in French must mean "buffer".

It looks like I was correct and not only does it mean "buffer" in the chemical sense, but also the computer science sense. (Babelfish is not much help because these are technical jargons. Google Translate, however, gets it right.)

I'm tempted to re-label all the bottles in the lab to make the American guys uncomfortable.

For a while we had Fetal Bovine Serum tubes labeled not only "FBS" but also "SBF" (suero bovino fetal) and "SVF" (sérum fœtal bovin)...the joys of working in a multicultural lab. It's also very cute to hear D (Colombian lab tech) and W (the French guy), who are a couple, talking to each other in broken English.

---

You know, I could just go and write 胎牛血清 (tāi níu xuè qīng) on all the tubes...

The marvellous limp

Steve told me a story about Honda's ASIMO robot, I don't know if it's true or perhaps applies to another humanoid robot, but it sounds entirely plausible. The robot was being shown off at some expo or another; in particular, its ability to climb stairs. Halfway up, one of the servos in a leg froze, and it fell over.

Then I thought: wouldn't it be amazing if someone designed a robot that could limp?

This isn't as stupid as it sounds at first blush. Limping, when you think about it, is an amazing behaviour. It's the ability to circumvent almost any non-critical musculoskeletal damage or defect in the legs and pelvis (chassis?) and keep going.

It is not something we think about consciously, which is amazing. If you get a rock in your shoe and don't have time to take it out, you will automatically alter your gait to put less pressure on that part of the foot. You can sprain your ankle and thereby limit its range of motion and the load which that leg can bear, or you can even fracture an important structural element like the foot or the tibia and if the situation is important enough, you will keep walking.

Even something as small and stupid as an ant, if you break off one of its legs, will go where it wants to go instead of wobbling around in a circle as a six-legged robot would.

OK...I just Googled it...robot limping has been looked into. We really need to know more about this if robots are ever to function usefully "in the wild". ASIMO will not be useful for taking care of housebound old folks if itself is also prone to falling down the stairs and lying there helpless.

Chickens for fun and profit

You know, I was going to write a proper blog post about this but I'm SOFA KING tired I'm just going to copy the contents of an email I wrote to my family.

I just got home at 9:15pm. I've had a nerve-wracking day due to the peculiar regulation that states that an egg which has not been pipped (hole poked in it by the chick) is not an animal, whereas an egg which has been pipped, even if you can only see a small SMALL point of beak sticking out, is an animal.

(Come to think of it, the US has similarly idiotic rules regarding what a human fetus is and how to treat it depending on whether or not it's inside the uterus.)

Anyway I was going to refrigerate some 20-day-old eggs today to kill the embryos, then cut them up. But, two of the eggs had been pipped. And not only that, they were making cheeping noises. So I had to call the RARC campus vet and ask her what to do. She said since they're pipped, I can't refrigerate them to death and instead have to CUT THEIR HEADS OFF straightaway.

Fortunately this only applied to one of them which was infected with my luminescent virus. The other one was the control and I half jokingly asked her if I could take it home as a pet. To my surprise she said yes.

Meanwhile I had a very boring day since I had to extract a lot of RNA samples.

And while I was doing that, the virus-inoculated chick almost cracked its shell half open! I picked up this rocking, cheeping egg and removed the shell. And then, I took this cute, newly hatched baby chick and cut its head off with a pair of scissors.

...it reminded me of the scene in Blade Runner where Roy Batty says to Deckard, "Wake up, time to die."

After cutting off its limbs and stuffing it in a 50 mL tube for deep-freeze storage, I took apart the rest of the eggs. Since they had been in the fridge from 10am to 8:30pm or so, they were quite dead. (On Monday I had found out the hard way that refrigeration for two whole hours is not sufficient to kill chicken embryos.) The beaks had pierced through the shell membranes, so they must have been breathing from the air pocket. A strange thing I noticed was that the yolk sac had at this point completely entered into the the chicks' bellies and become part of the intestine. Eggs are amazing things. They're like a little universe, a microcosmos.

Anyway...the other egg that had pipped is still in the incubator. If it hatches I'll take it home and keep it in my bathtub for a few days then I'll find someone to give it away to. Maybe just give it straight back to the campus Poultry Lab that I got the eggs from.

Immunology ain't English

Immunosurveillance is now an official English word, along with, apparently, "hellazpoppin'". Yay!

Microsoft Word spellcheck really hates scientific literature. I have the "check spelling as you type" option turned off on computers I use, otherwise any work-related writing becomes a sea of red.

The Braided World

Just finished writing an Amazon review of a good book (The Braided World) I read a couple months ago. Had to rant about two annoying characters though.

I picked up Kenyon's latest, "The Bright of the Sky" from the new sci-fi shelf in the local public library and loved it so I went looking for more of her work.

The book takes place in the aftermath of a cosmic disaster which somehow "stole" information from Earth, including information in the form of genetic diversity. As a result, the human race is slowly dying off due to a lack of resistance against various infectious diseases. A mysterious message is received, giving directions to a planet in another star system. A small expedition funded by a wealthy retired singer, Bailey (forgot her surname) goes off to check it out.

They find a very Earthlike world, inhabited by humans with one startling difference: they, and other mammals, are not viviparous. They don't get pregnant. Males and females both eject their gametes into "birthing pools" and the babies grow inside symbiotic waterplants. Eventually we learn that this planet was created as a giant seed bank by some other extraterrestrial Good Samaritan to preserve Earth biology till after the passing of the "dark force" and the strange reproductive system was set up to speed up the restocking.

Sex, being totally dissociated from reproduction, takes place casually and publicly between friends (however, penetration is considered disgusting), which startles the visitors from Earth at first. The rest of the book is an exploration of how human culture might develop with such drastically different reproductive biology, while the original mission to recover Earth's lost genetic diversity becomes almost peripheral.

Despite the beauty of this planet - "The Braided World" refers to both the riverine kingdom of the Dassa and the interdependency of humans and the birth plants - it's no utopia. The Dassa and their neighbours are just as flawed, brutal, and prejudiced as Earth humans. Occasionally girls with fully functional reproductive systems are born as throwback mutants, called "hoda". Upon their discovery at menarche, their tongues are cut out and they become mute (or so we think at first) slaves for the rest of their lives. Hoda's lib becomes a passionate subplot and a personal mission for Bailey.

Readers who enjoy SF with good world-building will like this book. Although Kenyon's skills aren't as mature as in "The Bright of the Sky", the braided world is a fully fleshed-out planet. You know it's good when you wish it was a real place you could visit. Like Octavia Butler's works, this is a more bio-driven SF rather than the majority physics-driven type of story. Kenyon doesn't get in over her head with the science or let it drown out actual plot. My only quibble is that the plant-dependent reproduction is at different points in the book said to be faster than normal pregnancy OR much less efficient.

The only two major characters I found unconvincing and annoying enough to somewhat mar the book were the anthropologist Nick Venning and the biologist Cai Zhen, who are both horribly stereotypical. Venning goes from being a wide-eyed kid who wants to go everywhere and do everything against the commander's advice (think Daniel Jackson in Stargate: SG-1) to being a raving murderous bigot after incautiously taking several doses of a psychotropic drug.

Zhen was annoying on two levels: one, that she's simply a mean person and every sentence that comes out of her mouth is a snipe. This could have been justified if her dialogue was humorously sarcastic instead of just plain vicious, or if she contributed something to the plot. I kept expecting some sort of shocking revelation, like her being impregnated by one of the Dassa, but no such luck. I felt like I had been led on since the other characters make a big deal of protecting her, as the only fertile Earth "hoda" - Bailey is postmenopausal. Even her extremely minor role in the story, sequencing the DNA of native organisms, could have been filled by a friendly robot (and I mean this literally; back here in the 21st century there already are robots that do that sort of thing). The other thing is that Kenyon seems to have subconsciously written in the stereotype of the ice-cold Chinese dragon lady. I'm not accusing Kenyon of racism (the diversity of cultures and persons in her novels is beautiful and honest), but of a worse crime for a novelist: writing a BORING CHARACTER.

Before anyone comments, I'm highly aware of the irony of a Chinese female biologist complaining about a book character who's a Chinese female biologist who complains too much... I'll stop now. Read it, it's a good book.

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.

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:

The Yeast of Malice and Wickedness

(originally written the day after Christmas)

My grad student Bible study group's doing St. Paul's first letter to the early church in Corinth, usually called 1 Corinthians for brevity's sake. Paul being Jewish uses the metaphor of leavened bread as "contaminated" and flatbread as "holy".

Your boasting is not good. Don't you know that a little yeast works through the whole batch of dough? Get rid of the old yeast that you may be a new batch without yeast—as you really are. For Christ, our Passover lamb, has been sacrificed. Therefore let us keep the Festival, not with the old yeast, the yeast of malice and wickedness, but with bread without yeast, the bread of sincerity and truth.

(reference: 1 Corinthians 5:6-8)

One of the new girls, a first-year student who's doing a rotation in a Saccharomyces lab, starts laughing. "I should label one of my freezer boxes 'The Yeast of Malice and Wickedness'," she says.

---

I'm having my own encounter with the Yeast of Malice and Wickedness today. In the morning I pull a flask that I'd seeded with quail fibroblast cells on Christmas eve, wash the layer of cells growing on the plastic with saline, then add some fresh M199 medium. I take another flask that I infected some days ago with my virus, scrape out the cells with a plastic squeegee, burst them to bits with an ultrasonic probe, and pipette a small portion into the new flask. I've done this five times over the past couple of months. Each new flask is infected with virus grown in the last one - this is called "passaging". What I'm trying to do is to get this virus to adapt to growing in cultured cells instead of the chicken embryos it prefers. Whole eggs are messy, fiddly, and largely unusable for genetic engineering purposes. It's a large DNA virus, so they don't evolve quite as fast as some others like the RNA-based ones, but I'm hopeful.

A few hours later, I come in to look at my cells and go OMGWTFBBQ as I realize that the myriad floating bubbles in my flask aren't just fragments of dead cells from the inoculum. For one, they're too small; for another, strangely opaque; also, joined together in short chains of twos and threes. My first thought is bacteria, but they're too small. I groan inwardly, contemplating the necessity of throwing this one away.

"Diana, can you look at this for me?" I ask, baffled.
"This is yeast," she says. "What medium did you use?" We pull the M199 bottle back out of the fridge. The medium is clear, unclouded by growing cells, but I groan again as I recall that I'd dropped the bottle momentarily that morning, letting the medium slosh up into the neck and cap. The cap of any bottle is always to be presumed contaminated, especially since these medium bottles are plastic which can't be flamed (passed through the flame of a Bunsen burner) like a glass flask.

"Maybe you can wash the cells and put fresh medium with antibiotic-antimycotic," she suggests. I do so feeling vaguely guilty. Cross fingers...

Next day the quail cells look okay, with no sign of the proliferating yeasts. But now I have malice against the stuff.

Multidrug-resistant infections in Sultanah Aminah Hospital

This is absolutely appalling. (Scroll down to the second part of the story in the middle of the page.)

If you don't want to read it here's a quick summary. A woman whose 60-something diabetic father was in Sultanah Aminah Hospital in Johor complained because a consultant told him he urgently needed a wound debridement surgery, but he was subsequently left in the multidrug-resistant isolation ward for five days with only i.v. antibiotics. He has a multidrug-resistant Acinetobacter infection in the ulcer. A reporter from theSun went to visit them and found that:

• The door of the quarantine ward had a sign saying it should be closed, but it was left open
• another sign said that everyone going in must wear gloves, masks, and aprons, but there weren't any masks or aprons
• there was a pile of used gloves next to the glove box (yay cross-contamination!)
• visitors were ignoring the signs since the protective equipment wasn't there
• even worse, the reporter saw A NURSE AND A DOCTOR!!! walk in, attend to patients, and walk out without putting on the PPE or washing their hands (and the doctor's tudung wasn't tucked into her lab coat, which is effectively the same as a non-Muslim doctor having unbound long hair trailing all over).
• Another guy was there who had been in a road accident and acquired a multidrug-resistant infection from a metal implant in his leg. He's been there with a FRACTURED HAND for over a month. His fiancee said that the quarantined patients appear to have been "forgotten".

This hospital is apparently run by monkeys. Even if the patients weren't KNOWN to have an infectious disease, clinicians are still supposed to wash their hands between patients (I don't use the same gloves for different experiments in the lab).

Let me point out again for the sake of my American readers that Malaysia is not, in terms of technology, resources, or wealth, a backward country. I take every opportunity to smack down the ignoramuses who assume that "developing country" = "1990s Rwanda". We make computers, other electronics, drugs, all kinds of fine consumer products. We have so much. But brains? Who knows.

Hi ho Silver!

I'm da Clone Ranger!

Also, found out today that our lab is going to get a virus from the UK that I've been waiting for for a really long time. It's going to speak ATGC with a Cockney accent.

2008 New Year's Resolution

I don't normally make New Year's resolutions (e.g. "I will not bite my nails" has been a historical failure since age eight or so) but I've come up with what I think is a viable one this year:

• To match any amount I spend aside from regular groceries, household, and toiletry supplies with donations to NGOs doing food aid, health, education, social justice, or women's issues - both secular and Christian.
• To match ALL spending on my cat with donations to animal welfare (not animal rights) and wildlife conservation organizations.

This way I'll probably spend less money this year on silly stuff and waste less time Internet shopping.

Maybe it sounds a bit extreme to some people but I've found since leaving home and starting to earn my own money at age 18, that the less stuff I buy, the less stuff I want. Materialism is a self-perpetuating lust, and most of the hobbies I really enjoy require very little material.

Other things I'd like to do:

• Write at least 2 short fiction stories and submit at least 1 to Writers of the Future or a science fiction magazine.
• Draw more, and spontaneously.
• Reinstall Creatures 3/Docking Station on my computer and start tinkering with the CAOS (Creatures Agent Object Scripting) language.
• Call parents and sisters and "small" boy more often (sometimes I forget my brother has a phone because he never calls me...)
• Clean my bike more often.
• Cook for my boyfriend and make him take his vitamins regularly.
• Watch more movies.

It's gonna be a personally interesting year...my project is going to get into animal studies...I'll have to write a thesis and hopefully graduate...my parents just got transferred to Penang...two of my London cousins are getting married in the summer so I'll finally have a chance to go to England...a couple of Phases kakis are getting married in Malaysia...another couple is having a baby, which makes them the first friends my age to reproduce...my boyfriend is taking 2/3 of a year off school for an internship...his mum wants to show our respective cats in the summer (TICA lets you show household pets)...

Et cetera. 'Tis life. =)

Public Service Announcement

Public Service Announcement: Cowpox is not vaccinia.
Cowpox is not vaccinia.
Cowpox is NOT vaccinia.

OK? Geez.

(this is something I didn't know either until I started working in a poxvirus lab...I wish "science writers" for lay audiences would stop perpetuating this inaccuracy. one hears it all the way through undergraduate. it's like Protestants thinking the Immaculate Conception refers to that of Jesus and not Mary (I thought that was the case until college too).

yes, Jenner did originally start "vaccinating" people with cowpox, but as the virus was propagated in cows, buffaloes, horses and other four-legged animals, at some point it was replaced with vaccinia, which is another poxvirus but genetically distinct. i.e. vaccinia isn't a derivative (descendant) of cowpox.

In case you're wondering what set me off, I'm reading Steve's mum's Christmas present to me, John M. Barry's The Great Influenza, about the 1918 flu pandemic.

Charles River Labs Christmas card

Charles River sent me a Christmas card...I'm kinda wondering why they bother to be politically correct in English by putting "Season's Greetings" but still have "Joyeux Noel" and "Feliz Navidad."

The funny part was the envelope: illustrating the dangers of using robots to address people.

Jef Mallet reviewing Pavlov

Quote of the day

Splitter: But there's no lab animal model for it.
Talaat: In the vet school, cows are considered lab animals.

(This was in the middle of a discussion about how to determine whether or not Mycobacterium avium subsp. paratuberculosis is the aetiologic agent of Crohn's disease in humans. If you click on the first link, the September 1 news article is the review paper that was under discussion. We kinda came to the conclusion that the only definitive way to determine this would be to kidnap a bunch of preschoolers and force-feed them MAP-tainted milk.)

So, uh, are you doing anything after the midterm?

I'm quite enjoying the Immunology course - there's enough new stuff to keep me engaged but it's (to me at least) simple enough to not make me sweat over Thursday's upcoming midterm. Last Monday, however, we had a "discussion section" in the evening outside class time, which the TA decided to make into a review session because a lot of people were confused.

After a very short time we came to the conclusion that he was a prat. I think most immuno newbies left more confused than they came in. As CS Lewis wrote of Eustace in The Voyage of the Dawn Treader, he "had never learned to tell a story straight". For introducing people to immunology you HAVE to tell it as a narrative - what happens when a pathogen enters the body. He was jumping all over the place spewing out blobs of unconnected, and often irrelevant, facts. I had an almost unbearable impulse to leap up and grab the chalk from him.

Anyway, the following email he just sent out has failed utterly to improve my opinion of him:

I hope your studying is going well (and just know that I’m around, and am flexible for the next few days if you want to get together). I also thought I would direct your attention toward the release of Matchbox 20’s new album, Exile on Mainstream. Anyway, it’s released tomorrow so you better appreciate that… or else.

Is he trying to ask the entire class on a date or what? *baffled*

The fate of tattoos

I'm taking Immunology this sem with labmate Angela and boyfriend Steve (and my poor engineer is going to die of acronym bombardment, he's not used to us biologists). So far we're going over the basics...classes of immune cells, the difference between adaptive and innate immunity and whatnot.

If you're a layperson reading this and want to know a bit about immunology I recommend Lennart Nilsson's dramatically beautiful The Body Victorious - you can see some pics from it here. He's most famous for A Child Is Born, which is the one that has all those neat pictures of fetuses.

Anyway, the prof today was talking about macrophages, which are big cells that eat things (you can basically figure it out from the name if you know Greek). One slide was about tattoos, and it finally answered the question I've been wondering about, which is why don't the macrophages eat up the tattoo ink and carry it away?
(Slide copyright Gary A. Splitter)

Actually, I like Sgt. Colon's explanation better (from Terry Pratchett's Jingo, which I think should be recommended reading for all citizens of any nation with a military):

"Sarge," said Nobby, as they looked out at the wonders of the deep.
"Yes, Nobby?"
"You know they say every tiny part of your body is replaced every seven years?"
"A well-known fact," said Sergeant Colon.
"Right. So...I've got a tattoo on my arm, right? Had it done eight years ago. So...how come it's still there?"
Giant seaweeds winnowed the gloom.
"Interesting point," quavered Colon. "Er..."
"I mean, okay, new tiny bits of skin float in, but that means it ought to be all new and pink by now."
A fish with a nose like a saw swam past.
In the middle of all of his other fears, Sergeant Colon tried to think fast.
"What happens," he said, "is that all the blue skin bits are replaced by other blue skin bits. Off'f other peoople's tattoos."
"So...I've got other people's tattoos now?"
"Er...yes."
"Amazing. 'cos it still looks like mine. 's got the crossed daggers and 'WUM.'"
"Wum?"
"It was gonna be 'Mum' but I passed out and Needle Ned didn't notice I was upside down."

Biasiswa Agong follow-up

For whatever peculiar reason, my post last year on interviewing for the Biasiswa Agong (King's Scholarship) is the first English language Google hit for "biasiswa agong", even above the JPA's page. This is sort of weird because I didn't get it (only 10 scholarships for MS and 5 for PhD are offered per year).

Anyway, a couple of people subesquently posted comments asking for advice (sorry for the delays in replying). Here's a short list of what I think I did right and wrong, hope it helps.

• In the letter notifying interviewees, they say to bring a hard copy of your proposal. Bring FOUR copies - 1 for each interviewer and 1 for yourself so you don't get confused.
• Also bring a copy of your CV just in case - if I remember correctly, the original application that we mailed in required one, but won't hurt right?
• Also bring a short outline of a verbal presentation of your proposal so you can rehearse silently while you're waiting. It's an interview not a presentation though, so don't make yourself a long speech.
• If you've been studying abroad for a while, PRACTICE YOUR BM!!! The interview was in English, but they asked a few sentences in Malay to check if I was still reasonably fluent. Pull out your long-forgotten SPM buku rujukan or whatever.
• Even if 1 interviewer does most of the talking, try to look at/address all of them while you're speaking. My interviewers were 1 Malay lady and 2 men; the lady seemed to talk most and to know the most about the subject I was discussing.
• Make sure you can explain how your studies/research will be useful to the rakyat eventually.
• If you're applying for a program abroad, be prepared with a convincing reason you won't just take the money and run (I think the govt is becoming a bit more aware of the brain drain problem even if they still suck at corralling the undergrad JPA scholars). And no, "my parents are getting old" is not convincing.
• Try to make yourself sound original and independent. This is where I think I screwed up - my current advisor/boss had just emailed me a big PDF of his grant proposal so I was sort of like "Er, yah, I'm just going to be the research assistant on this cool project..." *slaps forehead*

Good luck to you people who contacted me or who are reading this...let me know how it goes!

By the way, they suck at notifying unsuccessful candidates. I only found out when there was a newspaper article about the YDP Agong having lunch or something with the scholars. I can understand not notifying every Ali, Muthu, and Ah Beng who applied, but there weren't that many people who made it to the interview stage so at least could have sent out "We regret to inform..." letters right?

As for me...I came to the US anyway. I'm 8 months into a 2-year MS program. My salary and tuition are being covered partly by a scholarship from the institution I'm at (you know, "institution" sounds a bit like a mental hospital...) and partly by my PI's grant funding, since I'm working for him as a research assistant. This is generally what happens in the US for students in the natural sciences - funded either as RAs or TAs (teaching assistants, who teach undergrad classes).

However, if you're in bio like me and thinking of taking the same path to "the States", be warned that the NIH (National Institutes of Health), which is one of the biggest resources for life sciences research here, has been funding a smaller and smaller fraction of grant applications over the past few years, so your boss may run out of money for graduate student salaries. One of my lab-mates just lost her job due our boss pokai. So keep looking for other scholarships, and also for TA-ships and the like.

By the way - if you have any adik-beradik who want to study in the US for undergrad, tell them to apply to Williams College. Williams gives all international students a roundtrip ticket home annually. I almost fainted when my sis FlowerMoonFish told me. Bloody kid!

...under a gibbous moon

I got an email from Steve containing the phrase

Every Wednesday, someone sacrifices a mother rat..."

and to me it would have made perfect sense even out of context, even if I hadn't been asking after the rat, because I now think in terms of scheduling experiments, harvesting fresh cells.

...and then I realized that to someone else, we would sound like frigging Satanists =D

Also, I was going to reply to Steve's email and forward the relevant chunks to my advisor, but somehow I replied to the boyfriend and added el jefe's email by mistake. Which wouldn't have been terrible except that I signed off with "Thanks sweetie!"

So if you don't see any more updates to this blog, it's because I've ended my shame.

Terminally.

Bleep you like an animal

This is super funny. Apparently you can make female mice think they're males and try to hump everything in sight by removing their vomeronasal organs (either by genetic knockout or surgically).

Poor black mouse, the girl-on-top position doesn't work so well when you have four legs.

So sexual behaviour in mice is hardwired, but you can flip the switch:

Dulac thinks it makes total sense: "Instead of building a male brain and then a female brain, you build a mouse brain, and then there's a sensory switch that makes sure that the animal behaves appropriately according to its gender."

Let's not jump to any conclusions about the mutability or lack thereof of human gender, though:

It isn't clear how these findings might translate to other species. Many researchers think that the human vomeronasal organ is defunct, and the human TRPC2 gene is functionless.

"Different species use different sensory strategies to understand the world," says Dulac. She notes that whereas rodents use pheromones as an important trigger for sexual behaviour, primates and humans are more visual creatures.

Cancer vaccine - what??

Cancer vaccine trials for 230

KUALA LUMPUR: Some 230 advanced-stage lung cancer patients in the country will take part in clinical trials for a therapeutic cancer vaccine.

Deputy Health Minister Datuk Dr Abdul Latiff Ahmad said the vaccine, Epidermal Growth Factor (EGF), was the first of its kind in the world and produced here with the cooperation between Malaysia and Cuba.

“The second and third phases of the clinical trials would be conducted on 230 patients who volunteered to undertake the trials at 14 hospitals nationwide.

“They have been told they have about six months to live,” he told a press conference.

Dr Latiff said the trials would be conducted by a local biotechnology company and Cuban researchers.

(From The Star)

Ok, I'm really confused as to how EGF can be used as a cancer vaccine...as far as I know the therapeutic use of recombinant growth factors is in special bandages to heal chronic wounds like bad burns and diabetic ulcers. But I've spent all day reading Harry Potter so I'm not going to PubMed it now.

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I'm suspicious of "big" announcements with regard to scientific research in Malaysia because Malaysian officials like to say all kinds of karut stuff...like last week the Fisheries Department said they were going to save the vanishing leatherbacks by cloning turtles (can't access the original article because the New Straits Times is a lot more stingy about giving free access to archives). I mean, do you know how hard it is to clone mammals? Nobody's even TRIED reptiles yet...Junaidi can go jump in the lake with Michael Crichton and his dinosaurs lah.

Melaka

So Melaka, the place where I suffered for two and a half years before going off to college - also known as "an overgrown fishing village where everybody is related to everybody else", and by its Anglicized name of Malacca - is in the news again since someone discovered a new bat-vectored reovirus there. Apparently the Chief Minister isn't too happy about a virus being named after his state, never mind that nobody minded the naming of Nipah virus back in the 1990s (Chua Kaw Bing, the leader of the Malaysian team, was also involved in the discovery of Nipah, if I remember correctly).

Viruses have been renamed in the past, most notably the Sin Nombre ("No Name") hantavirus that killed a lot of people in a Native American community. The researchers were originally going to name it after the place it was discovered, but the community objected, not without reason since a number of their best young people had just died.

Thinking about Melaka again, I can't say that this is the only thing I find interesting about it. Melaka has a great history, but the vast majority of Malaysian local governments wouldn't know what history was if it bit them on the bum. The vaunted Portuguese fort, A Famosa is a pile of rocks while beautiful old Chinese shophouses that have been around for generations crumble (warning: 鸟屋 [The Bird House] is one of those artsy movies where the ending makes no sense).

During my time in college, I read Shellabear's transcription (it was originally written in Jawi) of the Sejarah Melayu [The Malay Annals - or loosely, "The History of the Malays"] and finally finished it during spring break of senior year. We had been exposed to snippets of classical Malay through the last two years of secondary school, but never read a full text like how American kids have to swallow at least one Shakespeare. I wanted to taste at least one classical Malay book in its entirety...which was pretty much the equivalent in difficulty of an ESL speaker digesting the Lord of the Rings.

I was volunteering on a Habitat for Humanity build that spring break. Lying on the bottom bunk in a beach house in South Carolina, reading by torchlight, I wept over the terror and betrayal of the Portuguese invasion:

Setelah datang musim maka kapitan kapal itupun kembalilah ke Goa. Telah datang ke Goa maka, diwartakannya kepada wazir-wazirnya peri kebesaran negeri Melaka dengan makmurnya serta dengan ramai bandarnya. Pada masa itu wazirnya di Goa Alfonso d'Alberquerque namanya. Maka ia pun terlalu ingin menegar khabar negeri Melaka itu. Maka ia menyuruh berlengkap kapal tujuh buah, dan ghali panjang sepuluh, fusta tigabelas. Telah sudah lengkap, maka disuruhnya menyerang Melaka. Maka Gonzalo Periera nama kapitannya. Telah datang ke Melaka, make dibedilnya dengan meriam. Maka segala orang Melaka pun terkejut menengar bunyi meriam itu, katanya, 'Apa bunyi ini seperti guruh?'

Maka peluru meriam itupun datang mengenai segala orang Melaka: ada yang putus lehernya, ada yang putus pinggangnya, ada yang putus pahanya, ada yang pecah kepalanya; makin bertambah-tambah hairanlah orang Melaka melihat peluru bedil itu, katanya, 'Apa nama senjata bulat-bulat ini? Mana tajamnya, maka ia membunuh ini?'

[My crappy translation: When the season came, then the captain of that ship returned to Goa. When he reached Goa, he reported to the viceroys of the greatness of Melaka, of its sovereignity and its many towns. At that time, the Viceroy of Goa was named Alfonso d'Alberquerque. He greatly desired to hear more of Melaka. therefore he commanded that seven ships, ten long ghalis [dunno this word], and thirteen fustas [dunno also] be equipped. When all was ready, he commanded the invasion of Melaka. Gonzalo Periera was the name of his captain. When they reached Melaka, they bombarded it with cannon. Then all the people of Melaka were shocked to hear the cannons, saying, 'What is this sound like thunder?'

Then the cannonballs came and struck the people of Melaka: some had their necks broken, some had their waists broken, some had their thighs broken, some had their heads crushed; and the amazement of the people of Melaka grew watching those missiles, saying, 'What is the name of these round weapons? Where is their sharpness, that they kill like this?' -- Sejarah Melayu, WG Shellabear edition, p.184]

That is the history of Melaka. The history of Melaka cannot be conveyed by a bunch of lazy vendors selling trinkets made in China. The history of Melaka cannot be conveyed by painting all the buildings in the historical district brick red. The history of Melaka, for heaven's sake, cannot be conveyed by a giant revolving tower shaped like Hang Tuah's keris.

The history of Melaka is the history of a fallen kingdom whose conquerors themselves all fell in time. It comes to us through stories, read or spoken, and through the lives of the people whose ancestors were there - Malay, Chinese, Indian, Portuguese. In comparison all else is dirt.

Nucking Futs

My friend Koidy, who's from Batu Caves and just finished her BS at Franklin and Marshall, sent me this story. Ooooookie. To treat erectile dysfunction? (Or as the less squeamish of us would call it, "impotence".)

Koidy brought up concerns about proper controls since the article says

so far 40 volunteers had tried the tablet and responded positively.

Perhaps it's just sloppy writing on the part of The Star - maybe Dr Kim did describe a controlled study but the reporter just thought it would be too boring to put in a mainstream paper - but otherwise it sounds sketchy. Also no mention of whether the results were published in a peer-reviewed journal.

This is a really irresponsible statement to make:

“Furthermore, because it is not a drug, it is safe for those with hypertension or diabetes, or (those) who have recently had heart bypasses,” he said, adding that some of the volunteers had undergone bypass surgeries.

Not a drug? The last time I checked, the general definition of a drug was any chemical that alters the body's physiology. If you claim that it can give fat old men boners by dilating their blood vessels, it's a drug. This also falls under the fallacy about "natural" remedies that technophobic types like to believe - that if something is natural, it must be safe. Another small molecule that can be extracted from nuts (cyanide from almonds) is "natural", but I wouldn't care to assume its safety in any great quantity.

Anyway, nitroglycerin is used in heart patients for the same purpose - it's converted into NO in the body. Why reinvent the wheel?

Also, something I might not have picked up on if I hadn't seen someone's letter to The Star about Malaysian academicians entering bogus design contests: the "International Invention, Innovation, Industrial Design and Technology Exhibition" that this product won a gold medal at is hosted by Malaysia. From the list of "winners" [PDF] from last year, it looks like virtually all the entrants were Malaysian. And there were FIFTEEN gold medals given out to university teams in the "Biotechnology, Health & Fitness" category, out of a total of 46 gold medals awarded to universities. It's like a primary school Sports Day where everybody gets a prize. (I was going to say "Special Olympics" but it's not fair to associate handicapped people with the incorrigibly incompetent.)

Check out the guy lah...see for yourself.

And whatever happened to Tongkat Ali?

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Stupid cat went out right before a thunderstorm. I have now one very soggy and unhappy kitty wandering around my apartment looking for things to dry herself on..aiyayayayayaya.

You know you're becoming a poxvirologist when...

Gah. I re-read Stephen King's Carrie last night and every time they talked about the "TK gene", instead of "telekinesis" I thought "thymidine kinase".

It really isn't as scary as it was when I was 16...

Poor little devils

So, now that I've gotten my 3rd and final Pathology 750 assignment grade back, I'm going to post the first one, which I'm proud of now but at the time was making me sleepless for a week. Since it was my first big assignment after not having had any science classes for 2 years, I was sick with worry after submitting it.

When I logged on to my uni's course content system and saw the 50/50 grade, it was a nearly orgasmic moment: I screamed. ^_^

Performing well academically makes me paranoid, though: it can't be that I'm that smart, I must be screwing up and picking all the easy classes. Low self esteem konon >D

Anyway, a quick run-down of the problem: Tasmanian devils get a peculiar cancer called Devil Facial Tumour Disease, which makes horrendous growths that swell, rot, and eventually cause them to starve to death. Theory is that the etiologic agent (i.e. thingy that causes the disease) is the tumour itself - since devils fight pretty much whenever they meet each other, chunks of tumour cells break off, stick to the new host, and grow on it.

People think this is possible because devils went through a population bottleneck at some point, so they're very inbred and therefore don't mount an immune response to each other's cells. Contrast this to humans who need to take powerful immune-suppression drugs if they receive organ transplants, even from relatives.

For the question we were asked to come up with an alternate theory (since reduced genetic diversity doesn't automatically transl