Baby in hospital

My computer's been sent back to HP to have the speakers and the monitor repaired, so no blog entries for the next week or so.

For the past week, I hadn't been blogging cos I'd been working on a presentation on fowlpox virus. I'll upload the PowerPoint when it's over...you all can learn about the wonderful world of avian poxviruses =) It'll be my first presentation in a couple of years, so hopefully I won't fluff it.

In the meantime, here are two short movies you should watch:

• The Laboratory Rat: a Natural History. Fifty Wistar (white) and Lister-Hooded lab rats were released into a fenced lot to see if they still had enough instincts to survive in the wild after 200+ generations of domesticatiion. It's a really cute series of short clips (total 27 mins) if you like little furry animals. It's enormously fascinating to see lab rats raised in "shoebox" cages on pellets learn to forage, socialize, hide from predators (one of the filmmakers' cats), and mate and raise pups. After a few months:

  "By now, the rats have learned to exploit food in the more remote places, and climb on small branches with great agility. [Rat falls off branch] Well, most of the time."

  
• Inner Life of the Cell. A collaboration between Harvard and Studio Daily, this is an absolutely beautiful short movie that departs from the typical biochem/cell bio/molecular bio "animations" of proteins represented by ovals and DNA represented by ladders. In the spirit of Fantastic Voyage, you feel like if you shrank down to the nanoscale and entered a living body, this is what you would see. The version with a musical soundtrack is here and the narrative version with labels is here.

Final

Today I waltzed out of my molecular biology final after barely half an hour - the first to leave.

This is notable because (aside from it being my first final exam in more than two years) I'm rarely the first person to hand in an exam. It's partly because my father's drilled into my head since primary school that one should always check one's answers, but also because...if you're the first person to walk out and you know others are struggling with it...you feel bad.

It's a form of survivor's guilt, a feeling that one's ability is undeserved and is morally culpable. My sis FlowerMoonFish, being both smarter and nicer than me, feels it more strongly. (Last year when she was taking A-Levels she said she studied extra so that the girls who actually needed to study wouldn't feel bad when they saw that she was mugging too.) It's an emotion that the jerky kids who like to suck up to the prof and wear their brains on their sleeves don't have to deal with.

But in the final analysis [hur hur hur], someone has to walk out of that room first. It's a nice day outside, might as well be me.

---

Last night I was explaining to Steve about in situ synthesis of oligos for DNA microarrays (see here, it's really cool):

"And who came up with that? A biologist or an engineer?"
"An engineer, but it was a biologist who came up with the application. I'm sure an engineer didn't wake up one morning and say 'I'm going to invent a way to synthesize oligos on a slide for fun.'"
"I don't think you can be a pure biologist or a pure engineer any more. You have to merge."
"Oh yeah? Let's merge."

^_^

EDIT: good GRIEF I'm degenerating into one of those girls who talk about their boyfriends all the time. The other night on the phone my dad asked me why I "have to be in a relationship all the time". Emotionally needy I guess =D

Introducing Lina

Hi everybody,

This is Lina. She was one of the third-year vet students' "practice" cats, so she was just spayed on Monday. She's about 1.5 years old, skinny little thing, nice and fluffy. So far she seems to be okay in my little apartment.

She's pretty laid-back, more interested in being manja-ed than in toys. A good cat for reading or sleeping. The vet students said she was so calm that they used her to test the dogs for cat compatibility. She knows how to do her "da bian" in the litter box, no problem.

Also, she has a tail which is as long as her torso and is as silky as those electrostatic feather dusters...oooh.

The name, in case anyone's wondering, is a reference to the monster with big teeth (which used to be a woman, and has the heart of a child) that follows Curdie around in George MacDonald's "The Princess and Curdie". Steve says he'd have named her Lilith instead, but I haven't read "Lilith". The name that the animal shelter originally gave her was "Kizzy" which I wasn't too keen on.

I've wanted to have a cat for a long time but despite having worked in a vet clinic I was sort of bemused by the amount of preparation it takes to have an indoor cat here...as opposed to the Southeast Asian method of "go out in the back alley and dump a bowl of rice on the ground". The adoption application form from the animal shelter was almost as invasive as the one I had to fill out to get my US student visa.

EXTRA SPECIAL BONUS BLACKMAIL PICTURE: Steve fondling my...kitty. Er, yeah, that's right...kitty!

Species

I was reading about the concept of virus species in the intro to the Virus Taxonomy Online site and found a statement that sounds a bit the stupid when you think about it:

It is remarkable that a century and a half after Darwin, there is still no agreement about what a species is.

Er...no it's not...because if Darwin's right that means living organisms are constantly changing, which is precisely why it's hard to put them in a nice box.

Fuzzy logic. 'S all good. =)

Not to mention dead organisms...I was Googling "finch pox" and somehow ended up reading about a debate about Archaeopteryx's relationship to dinosaurs. Evolutionary biology is cool but evo biologists spend so much time arguing with each other, which I don't have the energy for. The kind of stuff I'm doing, something works or it doesn't work, finis.

Especially viruses. It's been several days since I found out about reticuloendotheliosis virus (an itsy-bitsy retrovirus) piggybacking on bigger DNA viruses like pox and herpes, and I still think it's cool. Viruses have viruses??? It's like in the Jonathan Swift couplet:

So, naturalists observe, a flea
Has smaller fleas that on him prey;
And these have smaller still to bite ’em;
And so proceed ad infinitum.

Masuk angin keluar asap

I'm sort of glad Dr. Mahatir retired a few years back. He's got to be the only third world dictator ever to do so voluntarily. I'm getting increasingly convinced he's pretty nyanyok now though. Check this out.

The former prime minister said bloggers should not tell lies and untruths, and because there were no laws governing them, their freedom to write anything could negatively affect the development of the country.

“Although bloggers are not subject to the same laws governing the mainstream media, they should write the truth all the same.

And a few paragraphs later:

Dr Mahathir also apologised to Prime Minister Datuk Seri Abdullah Ahmad Badawi for accusing him of owning a house in Perth, Australia.

He said he got carried away when he mentioned it at a talk in Kulai, Johor, on March 29 recently and added it was based on a rumour.

Seriously lah...Malaysian public officials and politicians clearly don't know anything about the internet or they wouldn't have come up with such a hare-brained idea as registering "bloggers". There's clearly a difference between people with huge reputations who do it on a semi-professional basis like Jeff Ooi and idiots like me* who do it just to waste time, but it's along a spectrum. There is no discrete cut-off that would distinguish the "bloggers" the government wants to take down.

*Or Michael Ooi, for that matter (Just kidding. Read his blog, it's damn funny, and he's one of the more popular non-political Malaysian bloggers.)

Random lists of things

Things I own or owned that are older than me:

• My mum's swimsuit (it was actually quite nice-looking)
• My dad's Bible (pocket-sized copy of the NIV)
• My friend David's mum's old bike (a Motobecane Nomade, mixte-frame road bike. The photo in the Wikipedia entry is mine, actually.)

Things I like:

• Skinny boys (must work on Steve!)
• Sharp knives (I have 14 bladed instruments in my tiny apartment at last count, ranging from a foot-long Filipino bolo to a #11 craft knife)
• Medium-sized dogs
• Cats except brachycephalic breeds (e.g. Persians, which look like they've been punched in the face)
• Rainy days
• Broccoli, green peas, Chinese/Napa cabbage, Chinese radish/daikon
• Boston Cream doughnuts
• Automatic microplate washers
• Watching animals interact without human intervention
• Lindt and Dove chocolates, and those fancy Guylian hazelnut praline seashells
• Fireworks of any type
• Lego
• Complex but gramatically well-structured sentences
• My immediate family and most of the Hwa cousins
• White mice
• Wensleydale cheese
• Char koay teow and Penang laksa
• Microwave ovens
• Evolutionary psychology
• Thick copper wire, like the kind in the solenoids of ceiling fans

Things I don't like:

• Indexed shifters on cheap bikes (because the "clicks" on the shifters don't line up properly with the gears)
• Running
• Pipettors that take weird-sized tips
• Mustard greens
• Toy breeds of dogs (especially since working at a vet clinic in college)
• UMNO politicians
• Girls/women who wear a lot of makeup and expect males to carry things for them
• Radical feminists
• Ultracentrifuges (because I'm scared the rotor will come off and fly through a brick wall)
• Cotton rats, because they bite and they're tough bastards to catch
• Oscillating fans
• Cheap chocolate with palm oil or other vegetable oils substituted for the cocoa butter
• Whiny accents, particularly Malaysian Chinese-school-educated and the US "Valley Girl"
• Powdered latex gloves
• People who are stupid because they're lazy and/or arrogant (people who are stupid because of innate skill level are fine, it's not their fault...and they often act more sensibly than the former type of stupidos)
• Chee cheong fun ("pig intestine noodles")

OA research

About that Robin Weiss essay I blogged yesterday...something else interesting in it is that when he was trying to identify how far back in chicken lineages ALV (avian leukosis virus) became incorporated into the chicken genome, he went and stayed in the jungle with Orang Asli in Malaysia to take egg and blood samples from red jungle fowl (wild chickens).

I was interested to know if the chicken ERV was a recent introduction into domestic fowl, or whether it was present in the ancestor species, the red jungle fowl. In 1970, I made a field trip to Malaysia and lived with tribesmen (orang asli) in the Pahang jungle who knew how to trap these birds, in order to take blood samples and to collect eggs for cell culture.

This is one little anecdote, but it's a concrete illustration of how indigenous people's knowledge can contribute to science. No doubt if he had just gone there with a bunch of other urban-dwelling academics either from his UCL or from UM, it would have taken them months longer to find where the jungle fowl lived, develop trapping techniques, etc.

All the talk about biotechnology and bioprospecting that the government puts out is highly ironic in light of the fact that they're kicking some of these people off their ancestral lands, especially for a silly garden which is likely to be mismanaged and turn into a white elephant as usual anyway...

Really, really, retro

I was looking up feline leukemia virus on the Virus Taxonomy site for a reason that I hopefully will be able to write about later. Then I started browsing through the whole retrovirus section and remembered that I had been going to look up reticuloendotheliosis virus (it's something chickens get, don't ask) 'cos I need to find out if it's piggybacking on our fowlpox or canarypox samples. Then I got totally sidetracked because I found this cool paper by some old guy narrating the history of the discovery of endogenous retroviruses.

Science history is more interesting to read if you're a science student, I think, because it gives you an idea of the significance of technologies and knowledge you take for granted:

So the next step was to collaborate with Jim Payne to determine whether Env complementation and Gag expression were inherited concomitantly. Using inbred chickens, F1 hybrids and back-crosses, we found that both phenotypes were indeed inherited according to Mendel's first law and that they segregated together as a single locus [27].

My first reaction to this paragraph was "Why the **** didn't they just extract DNA from the chickens and run PCR on it to see fi the gag and env genes were there???"

Then I remembered...oh yeah hor, last time no such thing as PCR.

Nonetheless, the evidence that we accrued in the pre-molecular era has stood the test of time, and our hypothesis on ERV, which one reviewer described as 'impossible', proved to be correct.

And it's really impressive how much discovery got done back before the molecular biology explosion...like McClintock and her discovery of transposons by looking at blobby lumps on chromosomes under a microscope.

Back then...men were real men, women were real women and small fuzzy creatures from Alpha Centauri were real small fuzzy creatures from Alpha Centauri^*. Now we just buy reagents in kits and send our DNA samples off for sequencing and get a nice data file back.

*I think this is from Douglas Adams but I'm not sure.

National embarrassment

Good grief. I just found out from a commentor on the Education In Malaysia blog (see this story for background) that Malaysia was featured in Nature back in 2005. And not in a good way.

I know it's too easy to blame everything on the government...but that's because it is too easy. The idea of Ketuanan Melayu is a load of crap (as any idea of the supremacy of a particular ethnic group is, especially in a country with ethnic miniorities this big), and the resulting policies and practices are doing as much good for our country's progress as a pair of lead boots to a swimmer. See the Nature story here.

Inclement

What's wrong with this picture?

It's frigging April, that's what.

Lower lifeforms

I've come to realize that over the last 3/4 year or so (since leaving Madison last summer), both my motivation to do paid work and to write/draw in my "spare" time has close to vanished. Which is damn bloody suicidal for someone just starting grad school. Granted, there are other things that have delayed progress on my project (like my advisor being not around a lot and extremely scattershot as to what he wants me (and everybody else in the lab) to do; waiting for eggs to grow and viruses to ship, things under the control of biology and bureaucracy), but I'm having trouble focusing.

Part of it is fear - I don't have a good grounding in molecular biology yet - but my reaction to fear, doing nothing, is creating a horrible positive feedback loop, because if I don't spend time in lab, at least trying to work with viruses, design vectors, etc., I will learn nothing.

"Free" time has also been totally wasted because instead of making anything or even just reading good fiction/nonfiction, I've been spending a lot of time just surfing the Internet and shopping (mostly window) online. Turning into someone who shops as a form of escapism is turning into the very sort of woman I despise. I was planning to do something to enter the Writers of the Future contest this past quarter. I'm still thinking of a bunch of specific drawings that I want to do. I haven't saved anything in my writing folder or touched my sketchbook these past months.

A lot of this sluggishness is from last year when I was staying at home in Bentong. So, for future reference, being unemployed is very very bad for me and I'll need to make a rigorous program of stuff for myself to do - writing, drawing, reading technical stuff - to keep occupied the next time I find myself in that position.

Yeah...choking on self-pity atm.

Spam spam spam spam

It took me a while to realize this was a promotional website (clearly I'm not very observant) but it's a pretty funny game. I'm just sad that we're probably not going to get the collector's edition Spam cans (with Stinky French Garlic) in the US.

Supper's waiting on the table

Maundy Thursday: Just in case anyone thinks I'm pulling religious interpretations out of thin air, I've been told Billy Corgan is Catholic.

Speak to me in a language I can hear
Humour me before I have to go
Deep in thought I forgive everyone
As the cluttered streets greet me once again
I know I can't be late, supper's waiting on the table
Tomorrow's just an excuse away
So I pull my collar up and face the cold, on my own
The earth laughs beneath my heavy feet
At the blasphemy in my old jangly walk
Steeple guide me to my heart and home
The sun is out and up and down again
I know I'll make it, love can last forever
Graceful swans of never topple to the earth
And you can make it last, forever you
You can make it last, forever you
And for a moment I lose myself
Wrapped up in the pleasures of the world
I've journeyed here and there and back again
But in the same old haunts I still find my friends
Mysteries not ready to reveal
Sympathies I'm ready to return
I'll make the effort, love can last forever
Graceful swans of never topple to the earth
Tomorrow's just an excuse
And you can make it last, forever you
You can make it last, forever you

- The Smashing Pumpkins, "Thirty-Three"