Don't Shake the Flask

Because you don't know if it'll explode

Month: February, 2004

Odd Linkage:

Hundreds of coins found in patient’s belly. “French doctors were taken aback when they discovered the reason for a patient’s sore, swollen belly: He had swallowed around 350 coins — $650 worth — along with assorted necklaces and needles.”

The Pagan Hierarchy. This is amusing, but what’s the rationale for including scholars with wannabe witches on this diagram? They’re not really comparable.

News about Ender’s Game: The Movie. Well, this is the first I’ve heard of it. Ender’s Game is a good book but I wonder how well it will translate on screen. I just hope they don’t focus too much on the insect-like aliens. Practically every military sci-fi has insect-like aliens and that’s getting old.

The Thursday Threesome

Serendipity: Making fortunate discoveries by accident

Onesome: Serendipity:– Do you believe in destiny?

No. I don’t think one’s life is predetermined. I am in control of my own life and if I really wanted to do X instead of Y, I would do it. Nothing is stopping me, not my peers, not my professors, not my parents, not society, not God, or any other mysterious forces.

Twosome: Making fortunate discoveries– What is your greatest “find”? Is it an antique you discovered tucked away at a garage sale? Or maybe something as simple as the great sale on khakis or lawn mowers at your favorite store?

Well, I don’t like shopping except for books and “greatest find” depends on the time, that is, when I finally find a bookstore that carries the book I want. Yes, I can easily find it on Amazon, but what’s the fun in that?

Actually, what I hope will be my greatest find would be catching the local pen thief in the act. For the past couple of months, my pens have been disappearing from my desk never to be seen again. I have resorted to hiding my pen stash so they don’t disappear all at once.

Threesome: by accident– Have you ever discovered a place entirely by accident and it’s become a favourite place to go now? A hidden grove in the city park, a wonderful little coffee shop or restaurant, a treasure trove of a shop?

The stacks of the biomedical library. It’s cool as long as it’s not swarming with industrious med students.

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Links:

Scientists Accuse White House of Distorting Facts. Via a lot of people, actually. Prominent scientists issued a statement saying that the current administration is distorting science to favor its own policy. The original press release is located at the Union of Concerned Scientists. Here’s their report. And if you can’t get to it, here’s another link to the same thing.

The Pencil Pages. Pencil collecting. I used to collect pencils. I think I still have them somewhere.

WEBoggle. Word search on steroids. Play Boggle online, it’s timed and you get to compare scores with other online players!

Ack! Don’t Scare Me Like That

Or maybe I should just stop looking at my referrer logs. Sometimes I get referrals that look like a Really Famous Weblog has linked me. For about five seconds, I start panicking. How did they find me? Why did they notice? Will my host be able to accommodate all that extra traffic?

And then I look on the Really Famous Weblog’s page and there is no link back. Whew. Maybe the referral log is just picking up the site the visitor had on before or after.

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Links:

Well-Designed Weblogs Volume 2. Here’s the second installment of Lars Holst’s collection of good design. I don’t know how he does it, but he always finds the niftiest ones. Two years ago, all I had to go by was some “cool homepages” website that, well, left a lot to be desired.

Reading Design. I found this article in the comments section of the link above. Very useful.

A Certain Kind of Brain Power

I’m sitting in the back of the auditorium listening to a genetics lecture. Another TA sitting beside me is tapping away at her laptop. The other TAs are mysteriously absent. The rest of the seats around us are devoid of undergrads. The prof is meticulously explaining three-point crosses and my mind is going fuzzy at the edges. Needless to say, I’m not paying much attention until–

Student: So why did you figure that the “D” gene is in the middle and not, say, the “A” gene?

Prof: Pure logic.

The class erupts in laughter.

The prof was nice enough to explain the entire problem over again, but that got me thinking about logic problems. One thing I had always thought was cool about genetics was that the problems posed really are problems, that is, they usually require logic to solve. It’s not that I don’t think other areas of biology aren’t cool too, but other areas (immunology for one) require a heck of a lot more memorization than problem solving skills.

Maybe I’m just one big kooky geek, but I really like thinking about logic problems. Perhaps all the mental grinding required to solve one of those problems gives me the illusion that I’m actually learning something and becoming smarter. Memorization, well, what’s the use of that when twenty years down the road, you’ll have to look it up in the book anyway?

Version 2.0

Um, yeah, so I changed it again. And my mascot is back up. You know, I kind of hope the guy who drew him gets a deal to make stuffed toys out of his drawings. I’d buy one and put it in the window like a jack-o-lantern. Anyways, the design was inspired by a certain elegant-looking satire and humor site, and it might have been a ripoff if it weren’t for my dislike of columns of a certain size, a particular default font, and my lack of taglines. I used to have a tagline, but well, it was a stupid tagline. (Actually, it’s still around. It’s part of the title of this page, which I have been too lazy to change.)

Plastic and Animal Activists

One of my housemates has declared war on plastic. Actually, it’s not really a war–more like a boycott. She lectured me and the rest of my housemates about the danger of most plastics and that bacteria can grow on them even if you wash it several times. She’s thrown out everything plastic except the ones that say “5”. She says those are safe. Of course, she has read all about this in a magazine article that she can’t even cite.

Yawn city. I think she forgot that I work in the microbiology department. I’ve been to a multitude of seminars where bacterial growth on surfaces, particularly plastics, has been pointed out and accompanied by gross-out medical pictures. (There also has been talk about adding antibiotics to plastic, especially plastic implants, but at the moment, that’s going nowhere considering bacteria can become antibiotic resistant and grow on the implants anyway.)

But what I didn’t know about was the plastic numbering system. If you look for the recycling sign on a piece of plastic, you will find a number in the middle of that sign. It ranges from 1 to 7. The numbers themselves designate what kind of plastic was used. A quick and easy cheat sheet to what the numbers stand for can be located at Recyclenow.org. I’ve also found another article concerning the safety of plastic water bottles. Apparently #1 plastic is the safest while #3 may be the most dangerous.

And what about plastic #7? #7 is “other” plastic and is used to make those ubiquitous Nalgene bottles carried by college students, hikers, and ridiculously self-conscious yuppies. (I don’t own any Nalgene bottles, besides, why should I buy something that would make me look like every other drone?) The previous article mentioned research from a Current Biology paper that showed that toxins leached from compounds commonly found in #7 plastic were hormone disruptors.

And then there are those crazed animal activists who want to boycott Nalgene because it is the same company (you’ve heard of Nunc, right?) that makes research supplies–some of it used in animal testing. Personally, I don’t know any “money grubbing vivisectionists” but I bet these animal activists would feel differently if you told them that an animal model must be used to develop a cure for a disease they might have. After all, in vitro testing only goes so far.

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Completely Unrelated:

CN Tower Timelapsed. I like watching the moon move across the sky. This site also has some other cool stuff too.

Slaves found on Brazilian ranch. “Officials said they discovered 32 slave-workers on the ranch of right-wing Senator Joao Ribeiro in the northern state of Para. They said the captives worked seven days a week without pay and had no running water or toilets.”

Big bang busted in science class for high schools. I know everyone has been reading about the hoopla on the proposal to ban the word “evolution” in the Georgia science curriculum, but apparently there has also been other insidious proposals. Sometimes I wonder if creationists just want to ban science altogether and what would the world be like if they succeeded. It’s enough to make one cry.

Sidewalk-chalk drawings. They look so 3-D. Amazing.

Kylie Minogue music video “Come Into My World”. It’s a relatively old music video (2002), but what I find interesting about it is the repetitive filming technique. And is it just me, or does all the music by Kylie Minogue sound like they’re from the 70’s?

Star Atlases. Here’s a digitized collection of more old books, particularly those by Bayer, Flamsteed, and Reissig. There’s also an online exhibit on The Face of the Moon.

Fantasy Planes. Pictures of planes that look interesting and even beautiful, but never made it big due to various reasons.

The Godzilla Bug

A couple weeks ago, I was rooting around in different journals searching for the latest papers on virulence factors when I stumbled upon something that was so different and strange that I just had to sit down and say, “Huh?” This something in question was a paper by Angert and Clements on the reproductive weirdness of Epulopiscium, a bacterium that I had never heard of before.

When most people think of bacterial reproduction, they think of the asexual kind called binary fission. In a way, it’s like when your somatic cells undergo mitosis, the DNA replicates and then the cell divides forming two daughter cells. However, there are ways in which bacteria can exchange genetic material instead of making clones of themselves. In a transformation, you can shock the bacteria via a heat bath or electroporator into taking up foreign DNA. Or it could involve conjugation (“bacterial sex” if you want to get giggles from the undergrads) where one bacteria forms a pilus to another bacteria to exchange DNA. And yet a third way would be transduction where a virus is used as an intermediary (during an infection, the virus may take up some bacterial DNA so when it goes to infect another cell, that DNA will be transferred). Epulopiscium, on the other hand, gives birth to live offspring.

Live offspring?!

Okay, we’ll eventually get to that, but first let’s just consider, what is Epulopiscium?

The first species, Epulopiscium fishelsoni, was discovered by Lev Fishelson and colleagues while they were working on identifying the gut microflora of a surgeonfish species (Acanthurus nigrofuscus) in the Red Sea in the early 1980s. But among the gamut of symbiotic unicellular prokaryotes and eukaryotes, they found a gigantic cigar-shaped microorganism that could easily be seen just with a light microscope. This microbe, which was initially tagged as a protozoan, was covered in cilia and flagella which helped it to move around. Other Epulopiscium species were soon found as symbionts in other surgeonfish around the world.

To get a sense of how large Epulopiscium is, we should compare it to the “average” bacteria which can range from 0.2 to 1.5 microns. You would definitely need a microscope to see that. Epulopiscium is 250 microns long–large enough to be seen by the naked eye. But how can they get so large? A size of a cell is limited by how much material can diffuse or be transported through the surface to the interior. So a cell reaches a threshold when the interior or the volume of the cell increases faster than the surface area (consider the equations for the surface area and the volume of a sphere–the volume increases by r3 while the surface area only increases by a factor of r2). Epulopiscium gets past this rule by wrinkling or folding in its membrane to increase its surface area–not unlike the folds of mitochondria or the wrinkling of the brain.

Scientists, though, began to reconsider Epulopiscium classification. Was it really a protozoan? Pace et al. checked this by comparing genetic sequences rather than cell morphology. As a result, not only did they prove that Epulopiscium was a bacterium and not a protozoan but that it is closely related to another symbiotic bacterium, Metabacterium polyspora, which is found in the guinea pig gut as well as the more common soil bacteria Clostridium. This is going to be important later on.

So back to Epulopiscium and its unusual life cycle. Currently, it’s unknown how the bacterium is transmitted from fish to fish–it hasn’t been found in sea water or fish eggs or fish feces. The bacterium also follows a circadian cycle. During the day, it moves along the surgeonfish’s digestive tract, following the food and growing. At night, the bacterium reproduces giving rise to smaller cells which can go through the cycle again the next day when the fish feeds. In various species of Epulopiscium, the mother cell gives birth to one to seven daughter cells. The offspring grow inside the parent until they are so large that they burst through, killing the mother.

How did Epulopiscium come up with this bizarre birthing process? Its closest relative, Metabacterium polyspora, doesn’t do such a thing. But wait, Metabacterium as well as the soil bacteria Clostridium (famous members of this family cause botulism and tetanus), form endospores. Endospores form roughly the same way as Epulopiscium offspring, but they aren’t exactly live. They are dormant forms of the bacteria that are released into the environment when conditions are not optimal but start up their cellular processes again when conditions are favorable. Angert and Clements performed protein and DNA localization studies comparing Epulopiscium reproduction and endospore formation. And interestingly enough, both lined up. So what does this mean? Perhaps bacterial live births derived from endospore formation. Or maybe it was the other way around.

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More (Yet Unrelated) Links:

Takagism. A very cool locked room mystery. I hope the author finishes the next one soon.

4096 Color Wheel. Yep, another color scheme website. You can never have too many of those.

Dialect Survey Results. Geographical breakdowns of what people say and where they say it.

Links I’ve Accumulated in the Past Week:

Astronomers Spy Massive Diamond. “If anyone’s ever promised you the sun, the moon and the stars, tell ’em you’ll settle for BPM 37093. The heart of that burned-out star with the no-nonsense name is a sparkling diamond that weighs a staggering 10 billion trillion trillion carats. That’s one followed by 34 zeros.” The first thing I thought about was–space pirates!

After Packing M&M’s Together, Scientists Like What They See. “In possibly the biggest advance in the science of candy since the discovery that Wint-O-Green Life Savers emit faint blue sparks when chewed, scientists are reporting today that M&M’s pack more tightly in your mouth than gumballs.” It has something to do with the fact that M&M’s are flattened spheroids rather than perfect spheres.

Amazon Glitch Unmasks War of Reviewers. I read the book reviews on Amazon, but that doesn’t mean that I believe them. Sometimes I read a book that people call bad just to be contrary. And sometimes it turns out not to be bad.

Benign Viruses Shine on the Silicon Assembly Line. This has nothing to do with the viruses and worms spread via e-mail and networks. Real live biological viruses are used to grow crystals for technology that is becoming more and more miniaturized.

Desktop Is. Some screenshots of really ancient desktops.

Online Scrabble for One. I am such a horrible scrabble player. I think it has to do with the fact that the letters are mixed up and my brain isn’t optimized to be an anagram generator.

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Unconscious Mutterings

  1. Dragon:: Blood
  2. Molecule:: Of Water
  3. Tire:: Tracks
  4. Mighty:: Ducks
  5. Octane:: Fuel
  6. Troll:: Gate
  7. Atmosphere:: Pressure
  8. Guide:: Dog
  9. Leash:: Mania
  10. Dustmite:: Microscopic

So I’m currently hiding out in lab. I’ve been here most of the day and I haven’t been doing nothing, but well, I feel like I’m the only person in the world right now. I suppose I’m just being surly because everyone else is enjoying a three day weekend while I’m working but it’s not just that. And I can’t help thinking that this is all my fault somehow.

The Digital Poster

What does the background image on your desktop say about you? What does mine say about me? I’m not sure about you, but I think my tastes in wallpaper pretty much say I like to drift off into lala land. I definitely don’t like leaving my computer preferences on default, but once I do pick something, it usually stays for quite a while. I’ve had computer art, book covers, cartoons, and even scans of my own notes in a feeble attempt to rouse myself into higher productivity. Right now, my desktop looks like this. It’s from the Voynich Manuscript.

From the personal computers that I see in lab or around campus, most people have used photographs of places they have been or people that are close to them. And if not that, well, it’s a photograph of something. Are most people more grounded in the real? Or is it something a little more subconscious–that they are actually craving contact with the rest of the world while they are at their computers? And since a photograph would be the last thing I would put on my desktop, what does that mean for me?

Or maybe it means nothing at all. The desktop image is only a digital version of a poster on the wall. It can be taken down and replaced. It’s not permanent. And since it’s so easy to change, perhaps it reflects more of the computer user’s mood than his personality. So what do you think? What do you prefer to be on your desktop? How often do you change it? What do you think it says about you?