Don't Shake the Flask

Because you don't know if it'll explode

Month: June, 2004

Something New

So I installed Mozilla Firefox 0.9 on my computer today. Does anyone realize that it shows up as Netscape 7 on the referrer logs?

Anyways, I’m liking it a lot so far. I don’t know why I didn’t ditch Internet Explorer sooner except that the other browsers and the older versions of Mozilla Firefox (which was originally Firebird) just didn’t feel right. And for the record: I never liked Netscape. In some ways it was worse than Internet Explorer–for one thing, Netscape took a long time to start up.

The coolest thing about Firefox is that it automatically blocks those pesky pop-ups. Besides hating the autoclave, I also hate pop-ups and blocking them without having to navigate the insides of the browser or installing something extra earns a gold star in my book.

Addendum: Oh wow, when I went to do the spell checking in Blogger, the spell check box included a correction preview. That never showed up on MSIE.

I hate the autoclave.

The technicians are on vacation for the next three weeks so I have to autoclave stuff. If there was a possibility that I could have fobbed off the chore to someone else, I probably would have, but now I’m stuck with it. It’s not that I mind hauling things to and from the autoclave. I just don’t like turning the machine(s) on and off. I’m always afraid I might not have closed the door properly or I pressed the wrong button or something just plain broke down. Because, of course, there’s the possibility that the thing will explode. Especially while I’m in the vicinity.

I blame this on the first person who taught me how to use the thing by telling me autoclave horror stories.


Over the weekend, I saw the newest Harry Potter movie. All I can say is, “Eh.” It’s not particularly angsty, emotional, or scary. I wasn’t awed or anything. Even though this is a genre that I would normally get excited about, the entire Harry Potter franchise just leaves me feeling, well, blah. Maybe this is just my age and dullness showing.

I also saw all the episodes of an anime called King of Bandit Jing. I don’t know what’s with the literal translation–it should have been The King of Bandits, Jing or Jing, the Bandit King. Anyways, I found it excellent entertainment, especially if you’re not looking for anything serious. The main character is Jing, an unassuming teenage boy who no one suspects is the Bandit King until it’s too late. Jing is remarkably cool-headed, philosophical. His heists are more about challenge than profit. His sidekick is a lecherous bird called Kir. But besides chasing girls, Kir also doubles as Jing’s weapon by latching onto the boy’s arm and spitting out green fire. This anime is not about fighting, but the plotline is pretty non-existent. And taking into account the very strange fantasy/sci-fi settings, I concluded that the writers for this show were all on crack. Which was good, I suppose, since I wasn’t in a mood to appreciate anything that made sense.

Unconscious Mutterings

  1. Lounge:: Lizard
  2. Photograph:: Frame
  3. Catacomb:: Maze
  4. Crucifix:: Cross
  5. Fired drill:: Screw
  6. Tube:: Top
  7. Dropped:: Soup
  8. LTD:: Company
  9. Panther:: Cat
  10. Formica:: Tables

Reading Update:

Eternity Road by Jack McDevitt

The plotline of this sci-fi novel of post-apocalyptic Earth is that of the classic quest. The story starts in the Mississippi Valley in what used to be Memphis where the heroine Chaka, a young woman despondent over the death of her brother who died in an earlier quest to a place called Haven, receives a copy of Mark Twain’s A Connecticut Yankee in King Arthur’s Court from the sole survivor of that earlier quest before he promptly kills himself. Spurred by this event, Chaka gathers a band of unlikely travelers in another attempt to find Haven. In this future, humans are reduced to living in Middle Ages-like conditions except that the remnants of the past such as highways and train stations and even entire cities made by the Roadmakers are littered throughout the countryside. Haven, as myths from this fictional future say, was supposed to be a repository for books (extremely rare in this world) and the resting place of a fantastical underwater ship. Haven was also supposed to have the answer to why people escaped the cities and devolved technology-wise. I thought this story was only so-so; the author didn’t do anything original with the archetypal quest plot, and although the characters weren’t exactly flat, their development was rather predictable. Also, the answer to what caused the apocalypse? Mentioned liberally near the beginning and a total cop-out, the microbiologist in me grumbles at the virtual hand-waving that some airborne virus from the jungles killed most of the population.

Abhorsen by Garth Nix

The final volume of Nix’s Old Kingdom trilogy starts out, literally, with a bang and there are no rest stops until the end. The nineteen-year-old protagonist from the second volume, Lirael, with her nephew Sameth and two talking animals, the Disreputable Dog and a grumpy white cat named Mogget who definitely aren’t what they seem, race across the Old Kingdom and down south to Anglestierre (an early twentieth-century version of England where magic can’t work unless a wind from the Old Kingdom blows in its direction) to rescue Sameth’s friend Nick from a powerful necromancer intent on digging up an ancient evil. It’s typical fantasy fare on the face of it, but it’s world-building and character development at its best. I would recommend this book only if you’ve read the previous two, Sabriel and Lirael: Daughter of the Clayr. Lirael is not your typical fantasy warrior-woman. She’s unsure of herself, doubtful, melancholy (sometimes suicidal), and desperately yearns to belong. Sameth is whiney and a little spoiled, but while Lirael is a round peg trying to get into a square hole, Sameth is the square peg already jammed into a round hole and trying to get out. In other words, he doesn’t want to be what everyone expects him to be. And even if you despise coming-of-age stories, the fantasy world itself is worth it–who doesn’t want to be an Abhorsen, making the dead stay dead with the aid of magical charter marks and bells? (Aside: I’ve noticed that the publisher is coming out with “adult” editions of the trilogy. Those new covers with the simple artist’s rendition of charter marks are, to put it bluntly, ugly and puts me into mind of those adult editions of Harry Potter which are trying to appeal to the audiences that don’t want to be caught dead with a kiddie book. If you don’t want to be seen carrying a children’s or young adult book, you really haven’t grown up, have you?) And as for Mogget, the only character to have a solid appearance in all three books, readers won’t be disappointed when his true nature is finally revealed.

Currently Reading: All the books I’ve mentioned in previous weeks as well as How Dunk a Donut which is written by a physicist.

When Highway Robbery Pays

What is self and non-self? That question might drive philosophers and psychologists mad with hypotheses about ego, id, and the consciousness, but nature has figured out a way to distinguish us from the rest of the environment. The immune system.

Most of the time, we don’t even think about this part of ourselves unless we come down with a cold or accidentally trip and skin our knees. But our immune system is constantly on guard like the stations at a border crossing. Inspection is also a lot like what happens at those border crossings. If you want to get from Country A to Country B, you present your passport for the immigrations official to inspect. All the cells in your body have a sort of passport to identify themselves as “self”–the major histocompatibility complex (MHC). The MHC is expressed on the cell surface; the MHC itself helps present antigens. The antigen is like the photo and name on the passport. If the antigen is a self antigen, i.e. the cell’s own protein, then a passing immune cell like the T cell inspecting the MHC with its own T cell receptor (TCR) which acts like a passport scanner will let it go on its way. The TCR itself only causes the T cell to react and sound the alarm when it encounters a non-self antigen (like bacterial and viral protein).

Most of the time, this works like a charm. This is because T cells have to go to charm school before they’re let loose on the rest of the body. Charm school for T cells, however, is probably nothing like going to a finishing school in Switzerland. Immature T cells are sent to the thymus to be educated. As these T cells begin to express their receptors, the TCR is also tested for reaction with self antigen by a variety of antigen presenting cells. If the TCR binds to a protein made in your own body, the T cell that expressed that TCR would immediately get eliminated. The educators in the thymus know that it would be an extremely bad thing if the police force they’re training starts killing off their own citizens.

But sometimes it does go wrong, and as a result, we get autoimmune diseases like arthritis. There are some backup mechanisms to prevent this from happening, especially if a T cell that responds to self antigen somehow escapes the thymus. A T cell can’t be activated just by the TCR getting into contact with an antigen presenting MHC. Other receptors and ligands must also come together at the same time in a process called costimulation. Another backup plan is the Fas receptor. In the thymus, this is a mechanism to kill off the T cells that don’t come up to snuff. The eye cells also does this. If a rogue T cell wanders into the vicinity of the eye, the Fas ligand (which the eye cells express on their surface), will come in contact with the T cell Fas receptor. The result of this fatal meeting is the death of the rogue T cell.

A recent paper in Nature Immunology by Perchellet et al. describe another way in which our body establishes immune tolerance. This new mechanism, however, is quite unusual. Rather than acting as the classic border patrol official, some high-affinity T cells become Robin Hoods along the highways of the body.

The researchers used a mouse model to study multiple sclerosis, a serious autoimmune disease where the immune cells have gone haywire and have started attacking nerve cells. The problem arises when T cells start expressing a TCR that recognizes myelin–a protein that helps insulate nerve cells–escape from the selection pressures of the thymus and start proliferating. In studying the populations of immune cells in mice that make myelin and those that don’t, the researchers found a curious thing.

Normally, myelin (MBP, myelin basic protein) is only produced in the nerve cells. For educating the T cells, the thymus expresses a form of myelin called golli-MBP. Usually, this is enough to prevent any T cells that recognize myelin from getting out of the thymus. Sometimes, though, that doesn’t happen. Perchellet et al. generated T cells that respond to MBP by exposing them to a virus that was engineered to make MBP. But even without the selection pressure of the thymus, this was still not enough to generate a multiple sclerosis-like response in the mice. What was happening?

By observing the interactions of these T cells that could be activated by MBP, they found that these lower-affinity T cells were coming into contact with high-affinity T cells and the high-affinity cells are somehow stripping the other cell of their receptors without activating the lower-affinity cells or themselves. These Robin Hood cells perform the much needed backup service of preventing T cells that respond to MBP from proliferating, but they walk a very thin and dangerous line. This line of defense could easily break down–much like the Sheriff of Nottingham finally deciding to mobilize his evil henchmen.

A Little Bit On Schoolwork

Arg. I think I’m beginning to see the light at the end of the tunnel. The first phase of my qualifiers is almost done unless I get a total slapdown (or is that smackdown?) in the next week or so. The chair of my quals committee is optimistic though so…well, I’m not even going to try to speculate.

You see, the qualifiers are at the least, extremely nerve-wracking and stress-inducing. Because at the end of the ordeal, you’re either truly a Ph.D. student (which is why at the moment, I only call myself a grad student) or kicked out of the program with (possibly) the consolation prize of a master’s degree.

Summer Reading Lists. (via 2Blowhards) Darn it, do you want me to read the entire library? I yearn for that period in childhood when I hadn’t heard of recommended books and I got to wander around in a library or a bookstore choosing whatever I fancied. Actually, to some extent, I still do. I guess I should be glad I’m not taking humanities classes.

The Thursday Threesome

Capricious: Governed or characterized by impulse or whim, lacking rational basis or likely to change suddenly

Onesome: Characterized by impulse–Do you consider yourself impulsive or do you tend to think everything through before you make a move?

On the whole, I am not an impulsive person. If I were, then I still wouldn’t be able to elicit surprised reactions on the rare occasions that I am.

I hope this doesn’t make you think that I’m boring. (Or maybe it does.)

Twosome: lacking rational basis–If you are impulsive, do you rationalize and justify your actions? Like, since that item you bought on a whim was on sale, you really saved money by buying it?

No, I do not rationalize. I am fairly accepting of my own impulsive behavior. If someone else expects a rational reason for it, well, tough luck.

Threesome: or likely to change suddenly– When you make up your mind, does it stay made up or do you tend to change your mind at the last minute? …or do you waffle back and forth until you’re forced to decide?

I make up my mind at the last possible minute. This annoys the heck out of people who like to get things done early. It does not mean, however, that I’m constantly waffling on my decisions–I just like to take my time about it.


You know the one I mentioned before, the one who played obnoxious music? He moved out. The new neighbors moved in last night–I listened to them banging around as I fell asleep. Also, I know that they’re neighbors and not just a single neighbor because I saw two names on the mailbox. I’m guessing they’re a couple judging from the genders of the names (despite different last names) and the fact that their apartment is a mirror image of mine (only one bedroom).

Yeah, I’m nosy like that. But I’ll restrain myself from peeping in windows and knocking on their door to ask for a cup of sugar just to see how they decorated their living room.