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Wednesday, December 31, 2003 End of the Year Personally, 2003 has not been a defining year. It's one of those in-the-middle things in which it has been the same the previous years and will be the same these coming years. Or perhaps it just doesn't seem defining because life just flows along, slowly transitioning from one thing to the next. Those sudden jarring events which mark history simply pass me by, garnering no more than a blip on the news screen. Maybe in the future, I might be able to point to something that happened this year that "changed my life" but at the moment, I don't see anything. It's still too close to judge objectively--my reflective moods have a sort of reverse myopia. And as for resolutions for the new year, I have none. I don't intend to make any promises I can't keep. Blog-o-centric: Freewheeling 'bloggers' are rewriting rules of journalism. (indirectly via Reflections in d minor) The first thing I thought was "poker" but never mind me. I've been playing too many card games the past two weeks. The revolution should not be eulogised. (via Save the Snow) I think this blog falls into category "c" but maybe I'm being too optimistic. [posted by S. Y. Affolee on 2:55 PM : Be Pretty, Stay In Jail Cat shows, one would assume, would be one of those frilly affairs with the subtlety of a sledgehammer. Actually they, or at least the one I went to last weekend, are a mess of contradictions both plebeian and haughty, gaudy and faux-aristocratic--not to mention the pungent animal smell that greets the visitor despite the bottles of hairspray and shampoo and disinfectant on every grooming platform. Most of the room where the show was being held was filled with rows of tables draped with white paper tablecloths. On top of the tablecloths were cages covered in fancy satins and silks and velvets, but the fabric could not disguise the fact that these were metal cages with bars equipped with little more than a dish of food, a dish of water, and a litterbox. If the feline prisoner was lucky, he or she would also have a toy. On the cage were typically two signs: one with the name and one with the breed. Sometimes there would be other signs like "Do not touch." Some cages had cat pictures in little frames propped on top. All had cat grooming paraphernalia beside them. And it was somewhat amusing to think that these pampered felines have more cosmetics than the average female human. The first cat I saw was a Persian in one of the velvet cages. The gray-white puffball stared out from the metal bars with an angry look on his face. I would be angry too if I were trapped in a cage with a litterbox and for a brief moment, I contemplated unlatching the door. The rest of the room were dedicated to six judging rings. In each ring, cages--all white except for one side which was a door of metal bars--ringed the perimeter in a semicircle. In front of the cage was a table for the judge which contained a small podium to place the cat, a spraybottle of disinfectant, a book for notetaking, and a tray of ribbons. There was a placard below the podium with the Cat Fancier's Association logo, and the judge's name. Another table jutted out into the audience at a ninety degree angle. An organizer sat at this table taking notes with a stack of numbered cards in front of him. A young girl sat beside the organizer with a stack of paper towels and a large bottle of disinfectant. She would clean the cages after each round of judging. First, the organizer would place the numbered cards onto holders on top of the cages. 080, 081, 082, 083,... Each card would be either colored blue or pink depending on the cat's gender. The owners would place their cats in the corresponding cages and the judge would wipe his or her hands and the podium with disinfectant before taking out the first cat. Tails would be fluffed and fur ruffled. Balance would be tested and a toy would be dangled to catch the cat's attention to check other nebulous qualities. Some judges were more vocal than others in telling the audience what they were looking for, but in the end, the cat would be stuffed back into the white cage whether they liked it or not, the judge would place a ribbon on the cage and disinfect everything, and the whole cycle would begin again. Cat behavior in those little white cages is quite amusing. The older cats are used to the crazed show-and-tell of the circuit and just curl up in the corner and go to sleep. Others stand alert, posed and staring out at the audience, seemingly aware that at that moment, they are being judged. And the younger ones go completely bonkers, yowling their displeasure and attempting to chew the metal bars to freedom. Cat owner behavior is probably very similar to that of parents parading their kids in beauty pageants. Away from the ring, some of them are animated and eager to have photos taken of their cats. Others brush onlookers away in a snobby air. But once those cats are being poked and proded by the judge, they sit at the front row frowning or chewing their nails and flipping through a white booklet listing all the felines and their stats (not unlike obssessed RPGers) entered into the competition. And what is a cat show without the commercial stands selling flashy toys and grooming products and scratching posts covered in good quality carpet? I wasn't too surprised that they were selling fancy coverings for the cages but I did find the cat-sitting video rather ridiculous. Do people think that cats are like four-year-old children easily mesmerized by the television? Of course, there were also kittens for sale, and although no prices were listed, I had no doubt that these purebreds cost a whole lot more than one at an animal shelter. As a visitor and an observer, I find the whole ritual of a "cat show" rather strange and bizarre due to its fixation. An owner could easily spend a lot of money raising a show cat and the pastime/livelihood turns the owner into a particular "type." I'm not saying that the owners all look the same--they just have a particular attitude. The attitude of an obsessed fanatic could easily be found in other places such as trekkie conventions and political conventions and even a high school science fair, but its peculiarity in this case is emphasized by changing normal animal companionship to objectification. I don't think I would ever be a person who could ever do this sort of thing. Maybe I'm too soft in the head, but I would always think of the angry Persian in the velvet cage. [originally posted on 11:45 AM] [posted by S. Y. Affolee on 1:52 PM : Tuesday, December 30, 2003 A Question From Marvin: How come baby stuff only comes in pastel colors? Travel Waiting The problem with arriving early at the airport, sitting in a cramped airplane, and being squished into a bus that has turned into standing room only is the waiting. I hate being near strangers--actually, I hate being too near anyone, period--because I get nauseous from other people's body odors and I start getting paranoid when anyone looks my way. For instance, while I was waiting for the passengers from the previous flight to debark before I got on, a young woman and her husband came out of the gate. After she fiddled with her carry-ons, she looked up meeting my gaze and I could swear she smirked. Why? Well, maybe there was no why. Maybe she was looking at something else. But a few moments afterwards, I was still fuming. Because if she was indeed smirking at me, what was the reason? Was it because I was wearing an unfashionable coat and carrying an outrageous neon orange bookbag I got for Christmas with my hair sticking up in all directions due to static while she was stylish with her expensive coat and boots and Jennifer Aniston-like hair? The longer I waited, the more mad I got at people's general hang-ups with appearance. The woman in line in front of me was probably fifty-ish and she was putting on makeup. What's the point? Do any of the other passengers care? I don't think anyone looks that great with makeup. And if someone judges people through interviews or first impressions or whatever by whether or not they wear cosmetics, that person really has his or her priorities screwed up. And on a totally different note: do people's choices on reading material at the airport indicate anything about their personality? Most people were reading newspapers or magazines or novels by big name authors. I only noticed one person with any taste--an old man with a well-worn copy of The Name of the Rose. I wonder what the bible-thumping couple I ended up next to in the plane would have thought if I had decided to read the book I had brought with me instead of listening to CDs. [posted by S. Y. Affolee on 6:45 PM : Thursday, December 25, 2003 Merry Christmas and happy holidays! And don't get stuck on the computer all day! [posted by S. Y. Affolee on 12:16 PM : Monday, December 22, 2003 My sister tells me that she reads this blog and the thing she likes best (besides the "crazy" links I put up and my occasional mention of my "numbered" roommates) are the comments. Well, at least visitors will now know that their responses will not be in vain. We also tried making a chicken and mushroom quiche the other day. The trick is to not leave it in the oven too long or the chicken will dry out. Dried chicken tastes a lot like the dried meat stuff in plastic containers, the kind sold in Asian food stores. It's usually used to flavor rice porridge. I've also been writing for the last couple of days since I came home. I'm past the 25,000 word mark now, but the draft is really, really bad. It will never see the light of day in its present form if I can help it. I wonder if anyone has done a study to see what names would sell the most books or would induce a customer to pick up a book. We could have controls by having the same exact story with the same cover and the same title. Only the author's name would be different. Would a "John Smith" or a "Jane Doe" sell more books than a "Mortimer Granowsky" or "Shenesha Merhered"? Would any hint of ethnicity in a name alter how often someone would pick up a book? [posted by S. Y. Affolee on 12:14 PM : Friday, December 19, 2003 I saw Return of the King today. Let's just say I won't mind seeing it again, but I'll wait until the entire trilogy comes out in one boxed set with all the deleted scenes included before I indulge in another couch potato fest. It also snowed a couple flakes which sent some people into disaster frenzy. Ah, southerners. [posted by S. Y. Affolee on 5:12 PM : Thursday, December 18, 2003 Still Murky Dreams are always strange things--I can never tell if they mean something or nothing at all. I dreamed I was in lab and I would have never known anything amiss except for the stack of bills I found stuffed under the lid of an unused gel box. I did nothing as the money was obviously fake; Mickey Mouse was grinning out at me from the five dollar bill. And when I wandered back to my lab bench, someone had left me something--a basket of two kittens and a hamster that was outside of the basket. I found myself rummaging in one of the lower drawers and pulled out a camera and began taking pictures. It reminds me of the discovery of the structure of benzene and the dream about a snake biting its own tail. Yet I doubt my unconscious would be as elegant as that. I'm sure my own mind is messy with half-chewed ideas and partially formed solutions that probably would never work. Better yet, my dream mind is probably trying to trick me. The Thursday Threesome: The Christmas Song, Part II Onesome: Chestnuts-- Okay, just which Christmas food won't you touch? I mean, even when Auntie Sarah is serving it up with a big smile! Anything that smells weird or has too many artificial colors. Twosome: Roasting Then again, which Christmas food are you willing to risk life and limb for, even when Uncle George is between you and the platter? I don't really have a favorite Christmas food although I do like candy canes. The mint ones only, please. The pink bubblegum ones make me want to stick my finger down my throat. Threesome: on an open fire Heh. This line reminds me of a joke! Do you have a favorite bit of holiday humor? How about it? I don't have a joke although there was this one Christmas where my Dad and I calculated how much energy people were wasting from putting up Christmas lights on their house. I know, that's geeky, but you know, even though I don't remember the exact figures, the energy (and the money) wasted was quite significant. [posted by S. Y. Affolee on 8:22 AM : Wednesday, December 17, 2003 A Bit of the Mundane I've been trying to watch as little television as possible although I did catch the special on PBS about a group of enthusiasts who wanted to reconstruct the Wright brothers' first airplane. Ah, it would have been quite neat if I were so ingenious with bicycle parts, but I'm not that mechanical minded. While the program was blathering about the principle of lift, my Dad muttered something about Bernoulli's disk. Disk?! Well, if you think about it, a spinning CD when it begins to rise is simply another application of Bernoulli's theorem. Which reminds me, don't forget to backup your hard drive. I regularly backup my data, but hard drives themselves with all the seemingly confusing system files are equally important. And besides backing up hard drives, I've been writing. So yeah, I'm trying to be semi-productive during my break. 4096 Color Wheel. More color coding fun. PowerPoint Makes You Dumb. It also makes you sleepy. Very sleepy. [posted by S. Y. Affolee on 8:34 AM : Tuesday, December 16, 2003 An Older Generation My grandmother is a very stubborn woman, but I suppose being in her mid-80's that does give her some entitlement. However, this behavior gives my mother fits and she complains to me that she's being treated like a teenager. It's not surprising; occasionally my grandmother would pat my hand and say in awe: "You've grown so big! You were just a small child before." I suspect that's why she doesn't try to control me or argue with me. I'm still a baby in her eyes. My grandmother gets upset when my mother doesn't indulge in her every whim and instead tries to do things for her own good. This sort of stubbornness or disappointment that one's children isn't following one's commands stems from an ancient Chinese cultural belief of hsiao (or in Cantonese, hao). In the Chinese-English dictionary, hsiao is defined as "filial piety or devotion," but my mother just shakes her head and tells me that the simple English translation doesn't even begin to describe what it means for the traditional Chinese. One of the basic Confucian teachings is to respect one's elders. Because you were born from your parents, your hair is their hair. Your bones are their bones. Your flesh is their flesh. Hurting yourself would only hurt them. But somehow, this teaching had been twisted so that the head of the family is all that matters. Two parables illustrate the change. One is that of a little girl who sleeps outside of the hut and lets all the mosquitoes bite her instead of her parents. Another is that of the boy who must lie in the snow and go ice fishing because his sick father suddenly has the desire to eat fish. "This," traditionalists would say, "is how all children should treat their parents and respect their elders." I don't understand this sort of extremism. In a way, it's like living ancestor worship where the elders are treated like demigods and the younger members of the family must sacrifice themselves for whatever whim they come up with. This runs counter to my own thinking: shouldn't children be cherished or at least taken care of until they reach reproductive age? Why should the older members be indulged like kings when they've already reproduced? My question is, "If the elders are wrong, do you still have to do what they say?" According to hsiao, yes, even if it's your own life on the line. But I'm not saying that we shouldn't respect our elders at all. However, I think there is a line that you have to draw between respect and blindly following foolhardy orders. When one grows up and has his or her own family especially in a western society, it's natural to somewhat exclude the elders from meddling in how to run the household and life in general. There are also people who simply don't have the means of taking care of their parents. But I still think that western society can do a lot better than dumping the elderly into a nursing home. Western ideas about the elderly have trickled back east. In Taiwan, for instance, along with the McDonald's and Hollywood movies inundating every street corner, people have begun to not care about their parents. There have even been cases where siblings have sued each other for not taking care of the parents. But just as younger generations are starting to exert their independence for better or worse, the members of the older generation are growing due to today's better health care and lifestyle. So I don't see the problem changing any time soon. My mother once told me, "I hope I'm not that stubborn when I get that old." I'm not so sure it's the problem of stubbornness so much as that of independence. Although my relationship with my parents is quite different than the generations before, I expect no small amount of difficulty when it comes my turn to take care of the parents. [posted by S. Y. Affolee on 9:34 AM : Monday, December 15, 2003 Can one not pay attention and still be jaded? I had arrived at MHT early. Extremely early--three hours to be exact. But if I had waited for the next bus to take me across the state to the airport terminal, I would have missed my flight. So it wasn't surprising that everyone in the line during check-in were going to Florida and not to BNA. The woman in front of me was a grandmother off to see her grandchildren. She was going to be in Florida for an entire month and hoped that she wouldn't annoy her children by the end of her stay. In front of her was a little boy tugging a piece of luggage that was as big as himself. He asked me where I was going. "Are you going to fly?" "Yep." "Where are you going?" "Nashville." "Nashua?" "Nope. Nashville. It's in Tennessee." The little boy still looked perplexed. Nashua is a mostly residential town north of Manchester. The locals slur the town's name until it's only two syllables instead of the requisite Nash-u-a. And when I say "Nash-ville", I assume they only hear the "Nash" and immediately think of their local geography rather than some southern borough stuffed to the brim with energetic country stars. But they were off to a different gate and I was stuck at the end of the airport, deserted except for a cafe manned by two bored employees and a newsstand that was locked up. I decided to pass my time as I usually do whenever I'm at an airport, listening to maudlin soundtracks and reading trashy books--this time a trashy mystery book. I was well into the middle of the plot when out of the corner of my eye, I noticed people moving to stand in line at the gate. The older man and woman ahead of me said something that made me blink and I looked up to the television. It was on CNN and there were red-faced senators bellowing about the capture of a certain ex-dictator in the Middle East. And then before I had any time to digest anything, we were ushered into the plane--"We don't need to see your photo IDs at the gate," crowed the airline attendant. After take off, I fell into a tired stupor--I had little sleep the previous night--and would occasionally surface back to coherence when my head hit the cool window. I found more about the breaking news when I got back home, but after the first spiel, I was bored and disgusted with the news media. All the news programs were talking about it, rehashing the same details over and over again, only prepackaged in different (and over-the-top) metaphors. I don't only want to hear about teary wives at home or people cheering on the streets. I don't want all the gooey-happiness-oh-the-world-must-be-all-right from the news as well as those ubiquitous Christmas specials. I want my news cold, straight-up. But most places seem to serve it tainted. Ah well, I'll just predict that by the end of the holiday season, most people will be annoyed with the phrase, "We got him!" I know I already am just with how many times they played it last night. [posted by S. Y. Affolee on 10:11 AM : Sunday, December 14, 2003 Well, I'll be off in less than half an hour. No more New England boondocks for the next two weeks. Unconcious Mutterings
[posted by S. Y. Affolee on 3:40 AM : Saturday, December 13, 2003 Weekend Links: Daily Dose of Imagery. (indirectly via Monkeyfilter) Very interesting photoblog. Pretty women scramble men's ability to assess the future. (via 2Blowhards and Marginal Revolution) That sound you're hearing in the background is me snickering. But then I stopped snickering and went about trying to find the paper they referenced. The problem is, my school doesn't subscribe to Biology Letters. I found no mention of it on PubMed or on the Web of Science citation index. The researchers mentioned are into psychology, but the only work I saw cited on these indices were about spousal abuse and homicide (I found a publications list here, their 2002 paper has statistics on homicide rates). I've never heard of a journal called Biology Letters before so I queried Google, and the closest thing I got was some obscure Czech journal. What's going on? Did the New Scientist make up something or am I just not searching hard enough? Addendum: I finally found the homepage for Biology Letters here. You'll never find it if you don't search for The Royal Society as well. It says it's listed under JSTOR (another journal index) but I didn't see it. I think it's because the journal is still very new. Unfortunately, even though I found the journal, I still couldn't find the article--not even an abstract or a title saying it was going to be published. Researchers Say. (via Save the Snow) Well, at least we know this little piece is obviously satire. Word up. (I know I found this somewhere but I can't remember where exactly.) Interesting reviews, but I'm probably not going to follow any of the advice the next time I go shopping for a dictionary. [posted by S. Y. Affolee on 12:53 PM : This morning I finally got around to buying Christmas cards. Yes, I know this is sort of late for that kind of thing (I noticed a really long line at the post office), but I'm not going to be sending any of these cards through the mail. I felt really out of place among the frenzied upperclass shoppers on Main Street. I heard the term "el cheapo" being bandied about, but none of the merchandise being sold in Hanover were inexpensive. I think a more accurate term would have been "el too-expensive-for-normal-people-o". [posted by S. Y. Affolee on 9:25 AM : Friday, December 12, 2003 Sigh. More tales of woe. So this time I got to listen to Roommate #8 talk about her problems with her ex-roommates. And while a bunch of her med student friends and I helped her move in, I was treated to stories of psycho parents. Are all parents of med students crazy? [posted by S. Y. Affolee on 4:15 PM : Ugh. I feel as if my brain's been fried. This morning, Roommate #7 left to visit some of her relatives in New York City for Christmas. This also happens to be where Roommate #6 (or rather ex-Roommate #6) has moved to--let's just hope they don't bump into each other as their relationship from what I've gathered is less than congenial at this point. Another housemate is moving in tonight. I was just informed about this an hour ago by housing. Roommate #8 is a med student with an extremely Scandinavian name. I'm not a bad person to live with. Honest. I'm clean. I don't play loud annoying music. I automatically stay away from you if I sense that you're in a foul mood. I'm mostly at lab so I wouldn't be bothering anyone anyway. I don't think I'm part of the reason they all move away--but that's because I've heard more than my share of complaints about how school is treating them. [posted by S. Y. Affolee on 2:11 PM : Hugging. Do you like doing it? Do you do it often? I'm not the touchy-feely type so I only hug if the other person initiates it first. And even then, the whole thing seems really weird to me. Emotional rescues. I prefer my classical musicians to not have seizures on stage. When I was still taking lessons, I've had piano teachers tell me to express more emotion while playing--but I wasn't about to go flapping about on the keyboard. My view of performance is similar to that of the author of the article. Emotional music can simply be portrayed by how it is played and not by physical and functionless gestures. Addendum: And if people need physical cues to tell them how to feel at a particular passage in a piece of music, they've missed the point entirely. [posted by S. Y. Affolee on 5:45 AM : Thursday, December 11, 2003 Boom or bust? Or rather, the less confusing question the article is asking: are researchers in infectious diseases supposed to be happy because the government is pouring money into biodefense research? Obviously, getting grants for biodefense research has a lot of catches, and unfortunately, a lot of those revolve around fear. Mystery remains as journal withdraws paper. Recently, I noticed a lot of blogs talking about a Swedish student who supposedly partially solved one of David Hilbert's problems. I didn't pay any attention to it because 1) I've heard of Hilbert but had no real idea what he did; 2) I know no math beyond the mandatory two years of coursework I did during my undergrad years; and 3) the three math blogs/journals (each written by a math grad student, a math teacher at a high school, and a math professor) I semi-regularly read never mentioned it. This just goes to show that you shouldn't believe everything you read, especially if it's just linked by link-happy people and not by people who actually know what they're talking about. Health agencies scramble to counter Vatican's 'condom'nation. You can take the easy way out and ask the church, "Do you have proof that the AIDS virus can pass through latex? Where is your data?" But the problem here is that this is religion and that in a lot of ways calls for a mindset that is completely contrary to that of science. We have to ask ourselves, how can we deal with an group that cares more about regulating people's lives in how they see fit rather than gathering proof of their physical well-being? Deep Thinking about Weblogs. A little bit too much deep thinking if you ask me. What Not to Do When You Blog. Stupid rules. I thought the only rule was that there were no rules in weblogging. [posted by S. Y. Affolee on 5:54 PM : Growing Up and Pairing Off. Ah, very true. I don't know very many people currently who are in their early twenties (like me) but I know plenty of people who are in their mid-, late-twenties who either have significant others or who are lamenting about their lack of paired-ness and trying to do something about it. Like the author of the article, I am also Chinese but from here I differ from her in that I don't think of myself as traditional nor have I gone through dysfunctional relationships (more like lack of relationships altogether). Sure, it's depressing that people push the expectation that you have to be paired up every day. I sometimes get depressed too with how current society is set up. But I also know I don't have to put up with this crap. I'm not going to be the silly girl who pines away because everyone says the grass is greener on the other side (via Bud). I don't know what other people's reasons are for getting married, but I know that I will never do it because everyone else is doing it. I do science and I write. I love both of those things and I think I'm doing my part to contribute to a better society, not the status quo. I'm not going to let it change me to what it wants me to be. I have a better idea of who I am than a bunch of busybodies who only follow rules. [posted by S. Y. Affolee on 6:33 AM : The Thursday Threesome: The Christmas Song, Part I Onesome: The-- What is the "bestest" Christmas decoration in your mind? You know, the one that says, "This is Christmas!" The tree. This reminds me of Christmas (or rather around this time) during my first year as an undergraduate. At my "house" (sort of like a cross between a dorm and a frat house although it was less of a frat house than a dorm and everything was co-ed), the upperclassmen declared that it was annual tradition for the frosh to put up a Christmas tree on the side of campus's phallic symbol--the library. There's just one catch. The building is nine stories tall compared to the two or three stories of the other buildings. We went after hours to bypass the usual securities; some people stayed on the ground and other people went up to the roof so they could throw lights down and have the people on the ground tether them. By four in the morning, everyone was cold and annoyed and we didn't bother putting the big yellow "L" (because it stood for the house's name) up at the top because we were tired and we didn't want anyone to fall off the library roof. Twosome: Christmas-- What style of Christmas ornaments do you like to see? Are you a glass ball person? ...or how about that bow thing? Maybe Christmas Muppet characters everywhere? Hmm? When it comes to ornaments and the scale of minimalist to gaudy, I'm way off toward the minimalist side of things. Threesome: Song--...and your favorite Christmas Song? Is there one that just sets the season for you when you hear it? I mean, even when you're in a "Ho-Ho-Humbug" mood? A lot of Christmas songs annoy me because people have been using them as manipulative marketing tools. But if I had to listen to Christmas music, I'd prefer the really obscure ones that aren't exactly pretty--musically--to the ear. You know, the ones people would never play in a commercial or on the radio because they sound too ominous or depressing. [posted by S. Y. Affolee on 5:49 AM : Wednesday, December 10, 2003 Woohoo! I'm done with that paper/pseudo-grant proposal thingee that was due for my last required class ever (I'm not counting my teaching requirement as a class) and I only have three more planned experiments to do before I go on vacation and vegetate. Of course, this says nothing about the unplanned stuff that might pop up... [posted by S. Y. Affolee on 8:33 PM : A Brief Break You know, it's getting a little frightening with spam. Today, I got another one from a biotech company but this one sounds like they targeted me specifically because of the previous post (the one about influenza). Oh and the Nigerian scammers? The most recent version sounds like some Brits got into the act too. [posted by S. Y. Affolee on 4:23 PM : My 2.5 Cents on the Flu "Have we responded to these [infectious diseases] by better preparing for emerging disease agents, or are we continuing to act only as crises arise?" Thus a group from St. Jude asks in a recent paper in Science (a summary accessible to the public is in the Science Daily). Every year, health organizations urge people to get their flu shots. But why every year? You may ask. Why not once every couple of years like tetanus? The problem is that Clostridium tetani is fundamentally a different bug than the influenza virus. Tetanus has a double stranded DNA genome which is far more stable than the influenza RNA genome. Tetanus can immediately transcribe and translate the virulence factors (primarily the tetanus toxin) with relative ease and fidelity. On the other hand, with an RNA genome--well, to say the least, it gets a bit messy. In some ways, a bacterium is a bit simpler. Most, like the laboratory workhorse E. coli contain one loop or plasmid of DNA that contains all of their genetic information. This makes them very easy to manipulate. Viruses, however, come in a dizzying variety: DNA or RNA, double stranded or single stranded, and if single stranded, could be antisense (i.e. negative) or sense (i.e. positive). Influenza is a single-stranded antisense RNA virus. This means that before hijacking the host cellular machinery for replication, it first has to transcribe the antisense RNA to sense RNA with its own RNA polymerase. And for some reason, RNA polymerases are a lot more permissive of mistakes than DNA polymerases. To make matters worse, influenza doesn't have just one strand containing all its genetic information--it has eight. And what's even stranger, the virus leaves it entirely to chance for making new virions. In the host cell, the genetic material and capsid (the packaging for the genome) are replicated but are floating around within the cell like so many rubber duckies and sports shoes that have been accidentally dumped from a ship in the middle of the ocean. It is by sheer probabilities, then, that all eight different strands combine with the capsid to make an infectious particle. If the capsid contains the wrong combination of strands or is just plain empty, there would be no way for it to replicate. "Mixing" occurs when two different strains of influenza infect the same cell. With all the genetic material floating about, it is entirely possible that, for instance, the first three strands of RNA from virus A and the other five strands of RNA from virus B get packaged into one capsid. Reservoirs for mixing are commonly found in fowl and pigs that are kept in close quarters. Here, human and animal viruses can recombine and produce new strains that are fully capable of infecting human cells but express antigens (or surface proteins on the capsid) that have never been seen by the immune system. The Science paper mentioned earlier also described a new method for generating flu vaccines quickly. It uses the recently developed protocol for eight-plasmid reverse genetics to help engineer a vaccine seed virus. The reason why this is so new is the difficulty of the whole thing. You can't just zap the bug so it can ingest one plasmid with your genes of interest. For influenza, one also has to deal with the headache of putting eight plasmids in and this only works in a couple of cell lines, most of them in the possession of private pharmaceutical companies. A brief note on influenza nomenclature: So what's with the H's and N's and numbers associated with the different strains? One can't possibly memorize all of this. Are they just random "social security numbers" that are assigned whenever a new strain emerges? "H" stands for hemagglutinin which helps the virus infect cells and "N" stands for neuraminidase which helps the virus escape. Both of these are proteins found on the surface of the capsid. Aside from this, strains are also categorized A-E which also describe the surface of the capsid. A-E were originally differentiated by looking at the characteristics of the agglutination reaction when put into rabbits. Influenza A and B are the usual culprits during the winter time. Influenza A is the only one that has been further subtyped with HN numbers. Variants of each strain are also described by when and where they were isolated. For instance, the Asian flu pandemic was caused by Influenza A, subtype H2N2 (or more succinctly A/Singapore/1/57, i.e. type/origin/strain number/year). [posted by S. Y. Affolee on 9:01 AM : Tuesday, December 09, 2003 I Feel So Naive Now So...I found out that Roommate #6 had gotten arrested while she was still here. Shocked is too mild a term for my first reaction. Why did Roommate #6 never tell me (or any of the other housemates for that matter) about this? Well, I suppose people who've had run-ins with the police don't want to publicize it for obvious reasons. This may have accounted for her strange absences which I didn't pay much attention to in the first place, however, she is gone now. But darn it, I lived with a delinquent and didn't even know it! (And to think that Roommate #6 thought that I was a lot like her--the only way I got along with her was that I wasn't like her.) [posted by S. Y. Affolee on 9:11 PM : I got my first spam e-mail from a biotech company that addressed me as "Dr." instead of "Miss" and I felt like I was tossed into some parallel universe where I was actually sitting at a desk in an office somewhere with a lab coat and a mustache. If I feel like that now when being addressed as a doctor, one wonders how I'll actually feel if/when I really get a PhD. Abercrombie & Fitch's Blue Christmas and The Look Of Abercrombie & Fitch. I find their business practices abominable. I guess they're going for the niche market of young, white high school and college students, but they've got to rethink their strategy if they're attracting lots of disgruntled minorities. Besides, I find it really weird that they have naked men plastered in their stores. Maybe what they really want to sell are sex toys. Really funny (at least to me, anyway) movies: Twisted Chipmunk Song and Lord of the Badgers. Canadian flag causes flap in the U.S. What I don't get is why they conducted focus groups for this kind of stuff. And why can't Canadians display the flag of their citizenship? Nobody says anything when Americans deck themselves with flags. [posted by S. Y. Affolee on 7:15 PM : Monday, December 08, 2003 Taboo. In my results, they basically told me that I was inconsistent with my beliefs. I really don't like to be told that I'm not logical. Compared to other people, I am more likely to see something as morally wrong and recommend prevention or punishment for it, although I would see something morally wrong regardless of culture or societal norms and not because of it. [posted by S. Y. Affolee on 7:54 PM : ARG! I insisted that politics and technology were inseparable. Hey it's nice to be right. (via Allied) Somebody tell this guy he's off his rocker, even if he is employed by a certain Ivy League institution. [posted by S. Y. Affolee on 6:36 PM : On a personal note: So Roommate #7 arrived today and boy do I feel emotionally sapped. Already I've been relegated to the role of "sympathetic listener" as I'm inundated with tales of woe--especially of the boyfriend kind as well as disillusionment with Roommate #6 (I didn't ask how #7 knew #6 in the first place). I was going to talk about an article that I had stumbled upon and ruminate on the conundrum of women writers trying to be well-known but could only do so with the help of men who are already established in the "elite" but--well, you do know the feeling of having your brain going non-functional don't you? Maybe I'll talk about it tomorrow if I get my energy back. Geez, too many people problems. [posted by S. Y. Affolee on 6:08 PM : Sunday, December 07, 2003 Darn it, why does the weekend always go so fast? I was hoping to get more done but in reality I haven't gotten anything done. Must be those crazy neighbors constantly slamming the doors and disrupting my concentration. To make the evening go by even faster: Free Flight. Very fun, but beware if you easily get motion sick. Have Snow Shovel, Will Travel. But how helpful will it be if you get rerouted to Baltimore? Der Mensch als Industriepalast. Did I spell that right? I don't know any German, but this is one cool poster. Long Bet. Which reminds me of the time when Stephen Hawking and Kip Thorne came over to have dinner with the undergraduates (back when I was attending Geeks U.) and made a bet about the existence of time travel. [posted by S. Y. Affolee on 3:35 PM : I'm finally alone. One of my housemates left last week for a month long vacation. The other housemate left this morning, probably for good. She's off to do an independent study--on weblogs. This morning, I stood at the window looking into the clear sky. I couldn't discern any snow falling, but the wind was fierce, bending back the trees and sweeping up the snow that had accumulated on the roofs so that the air was obscured by a thin white veil. At last, no more annoying phone calls from somebody else's chatty boyfriends. Edit (Noon): Sigh. Nevermind. Just got a call from the new housemate (henceforth known as "Athena" on the decoder page because her real name is an alternate form) saying that she's coming tomorrow. There's no avoiding anyone, even if you want to. Unconscious Mutterings
Originally posted at 9:40 AM. [posted by S. Y. Affolee on 2:15 PM : Saturday, December 06, 2003 Those Crazy Links Women With Big Boobs Are Smarter. Which is another indication that you should never believe anything that Yahoo! news posts. It's a made up story from a tabloid rag--the researcher doesn't exist and there are no papers of the kind in the journal databases (I know, I checked). Which Historical Lunatic Are You? My result was Ludwig II, the Swan King of Bavaria who was declared insane and confined to his bedroom by concerned (and embarrassed) subjects, but escaped and later found drowned with his physician in Lake Stamberg in mysterious circumstances. GodChecker: Your Guide To The Gods. They have an odd way of describing deities. But I still prefer the Encyclopedia Mythica for looking up anything mythology related. Devoted Bee. Nifty illustration site. Ban Comic Sans. Well, I wouldn't go so far as to get rid of it altogether or to bash the creator of the font (after all, he was just doing his job), but 99.9% of the people using Comic Sans should be figuratively shot for inappropriate font use. For starters, people should stop using it in powerpoint and web design. Well-Designed Weblogs. Arg! Now I want to totally redesign this site. Actually, I've been fiddling around ever since the latest version of this weblog came up. I've gone through about ten templates so far, but don't expect any sudden changes in the next, oh, three or four weeks. [posted by S. Y. Affolee on 8:34 PM : Impracticality I really don't like physical pain or discomfort. There are, of course, people who say that it'll make you a better person if you endure pain and discomfort but I'm not a masochist and I don't think I'm invincible. And I hope I'm not that stupid. What I don't understand are all those hard core joggers who run around in subzero weather with nothing on except some spandex. I also don't understand why some students walk around in blizzards with nothing more than a sweater. Like this morning. I only walk around in blizzards if I'm wearing my big winter jacket (the same one that old ladies make fun of because it's not "fashionable") and if I have errands to do. If I don't have errands, I would just stay at home and drink hot cocoa laced with caffeine. [posted by S. Y. Affolee on 8:04 AM : Friday, December 05, 2003 Two Kinds A person may claim that one is unique, but particular behavior may be widespread. I find these similar behaviors curious, fascinating, and also at times, downright annoying. People with significant others talk more about their significant others than about themselves. They skirt around the subject of themselves. It's as if they've pushed their own personalities under the rug. "My wife did this" or "My boyfriend did that." Are they trying to prove their fidelity and love for their spouses to others? Or do they just relish saying "my --insert significant other here--" as a sort of possessive idiosyncrasy? I should start tallying up how many times these people start their sentences with the word "my". I'm also tired of meeting so many young Asian women who think they are being individual by being angry and foul-mouthed. There are already many people in the world who are angry and foul-mouthed and I find it neither interesting nor unique. Perhaps they think it's a way of rebelling against the stereotypes of meek and accommodating or strung-out overachiever, but in fact, they're just creating another stereotype for themselves. And I don't think the much blogged about comedienne who makes money using this attitude is helping matters much. Not So Random Linkage: Stewardess Uniform Collection. That's a lot of uniforms. And a somewhat disturbing obsession. Oneword. You have sixty seconds to write anything about a random word. A good way to get past writer's block. Eat worms - feel better. It sounds gross, but there is some logic in this. The thinking is that the worms do or produce something that suppresses the immune system from overreacting. This is somewhat similar to the bacteria in our gut--these microbes help us in digestion and make our immune system tolerate certain foreign agents that we come in contact with every day. It also helps keep our immune system robust. Studies have been done in mice where animals kept in a sterile environment their whole lives were found to have lower white blood cell counts and an atrophied thymus (the organ that produces T cells) compared to their counterparts in a regular cage. [posted by S. Y. Affolee on 7:07 PM : Brainwashing Or Just Innocent Illusion? Around this time of year, some people worry about disillusioning their kids--specifically the fact that there is no Santa Claus. People also worry about kids finding out that the tooth fairy or the Easter bunny don't exist either so there much be something about retaining illusions during childhood. Personally, I don't like the idea of duping kids into believing the existence of imaginary beings just as I don't like forcing kids into the same religion that their parents are in simply by the virtue that they are their parents. Of course, there will probably be adults that will argue with me that kids are young and impressionable and should be "guided" in a manner that their parents deem proper. They will probably also argue that I'm a childless twenty-something who has no place in telling other people how to raise their children. But I'm not telling anyone how to raise their kids. I'm just uncomfortable with the fact that people find it perfectly acceptable to tell other people what to believe despite the fact that these people have brains like everyone else. The only difference is that they're younger. I'm quite sure that most people who can still recall their earliest memories will be hesitant to say--did this really happen? Fantasy and reality don't have the same boundaries as they do when you're older. You're never sure that the particular thing that happened when you were three actually happened or was something that you wanted to happen or just a dream. People who insist to kids that Santa Claus is real will only prolong this uncertain stage until they're much older. Then who is to say that you can't question your entire childhood? When I was in fourth grade, I once had a neighbor who was a few years younger than I was. I mentioned that Santa Claus didn't exist and she went rabid on me--telling me, yes, there was a Santa Claus as well as the tooth fairy and the Easter bunny and who knows what else. I shut up after that since it was obvious she was never going to believe whatever argument I would come up with. And now that I think about it, that sounds suspiciously like religious people or people who believe whatever the government tells them. Maybe adults aren't that much different from gullible children. [posted by S. Y. Affolee on 5:49 AM : Thursday, December 04, 2003 Don't you just hate those people who complain about assignments but they're already done with it a week beforehand? Ugh! These people have no idea what the meaning of procrastination is. (As you can guess, I have stuff due for classes in about a week and classmates are complaining to me about assignments they've already finished. I'm not even half-way done yet!) The Thursday Threesome: White Christmas Onesome: I'm dreaming of a white Christmas- Are you hoping for a white Christmas this year, or are you somewhere you seldom see snow? Up in New England (where I am now), it's been snowing since December 1. However, I'm going back south for the holidays so the chance of literally having a white Christmas is slim to none. Twosome: With every Christmas card I write- Have you begun the cards? Do you write a personal note in each one, or just sign a generic greeting and your name? Or maybe print out the ol' yearly form letter to let everyone know what's new for you? I am really bad about Christmas cards. I give cards to my close relatives and that's it. I could send some to my friends from my undergraduate years or my former roommates, but I have absolutely no idea what their current addresses are now. (Of course, I could find out, but I'm too lazy and it'll seem too much like stalking. Besides, they don't know where I live now and it's not like I get any snail mail aside from junk mail anyways.) And I generally just sign cards. It's too much work to be personal and too fake to send a form letter. Threesome: May your days be merry and bright- What do you do for the holidays to ensure they'll be merry? Sleep. That seems to do the trick for a lot of things. [posted by S. Y. Affolee on 12:30 PM : Wednesday, December 03, 2003 Wait a minute. There's a DNA sequencing kit for kids?! Okay, maybe I should have seen this coming, but wow. This is one of those things I would have done anything to get when I was younger. [posted by S. Y. Affolee on 7:29 AM : Wizbang 2003 Weblog Awards. So I was playing a game with myself to see how many of the nominees I recognized. Quite a few, actually. And I was thinking--what if I make my own "weblog awards"? But then anyone of importance who would get nominated would be way too insulted at the imagined implication that some backwater blog like mine would think they need any more attention from nobodies. Plain English Campaign. You know, I like the idea of writing clearly so people can understand what you're trying to get across, especially in the field of science, but I also don't want to sacrifice vocabulary for simplicity. I can easily imagine people taking this too far and limiting our language to, say, 200 words just to express necessary concepts. Sometimes, complexity can be a good thing. [posted by S. Y. Affolee on 6:40 AM : Tuesday, December 02, 2003 Are We Responsible For Creating Superbugs? In a recent Science paper ("A Bacterium's Borrowed Weapon" is a simplified summary), a collaboration at the CDC and the University of Michigan determined the probable mechanism through which Staphylococcus aureus acquired vancomycin resistance. Vancomycin, if you're not familiar with it, is one of those drugs you use as the last resort and if the infection is resistant to it--well, to say the least, you're in big trouble. So far, though, the vancomycin-resistant strain of S. aureus (or VRSA) has only been isolated in Michigan so the general public doesn't feel like it has to worry. Yet. But that's the problem. Most people don't feel the need to work on interesting and potentially dangerous problems unless it has affected most of the population or some famous person with a lot of clout. So how do microbes, specifically bacteria, become resistant to all these drugs? I think the answer to that question is quite simple--they become resistant because we select for them. Let's say a patient has a bacterial infection. In this person, there is a population of bacteria that is growing uncontrollably. The person's immune system may or may not be able to contain it in time. The doctor then gives the patient a drug. If the drug kills 99.999% of the bacteria, the 0.001% that remains alive because they are resistant could expand again--but this time giving rise to an infection that cannot be eliminated through the original drug. The same thing will happen to whatever else we throw at the bug. Well, why don't we just develop or find new drugs or modify old drugs? First of all, there are only so many targets that a drug can hit: cell wall synthesis, DNA replication, RNA synthesis, antimetabolites, protein synthesis. There is also the problem of selective toxicity. Drug X may kill the bacteria, but it may also kill mammalian cells as a lot of cellular machinery has been conserved throughout evolution. The thing is--if we come up with something to solve the problem, nature probably has already figured out a way around it. And even if a drug can be found to target one particular bacteria, it wouldn't be a very practical drug in the viewpoint of a practicing physician. Doctors are afraid to be wrong and would rather throw a drug that can act on a wide variety of diseases rather than one specific one--because if the disease isn't that one specific one, the life of the patient may be in serious jeopardy. There is currently no definitive solution for this problem. And one must admit, the problem is actually being exacerbated rather than relieved by the elaborate cocktails of drugs being produced for immunodeficient diseases such as HIV. So what can we do? We can start screening through libraries of chemical compounds, for one. But I personally don't think we'll be able to outwit nature unless we think of a completely different way of approaching the problem besides just going one by one through different compounds that a bacterium will certainly get over. [posted by S. Y. Affolee on 5:44 PM : Whenever I see a wishlist or gift registry on someone's website, I get really irritated. I mean, in principle, I shouldn't be. People are allowed to do whatever they want to their websites. If people want to take advantage of others' generosity to get ahead, I guess that's fine too, in a dog-eat-dog kind of way. So I suppose I'm old-fashioned in one sense. I want to be able to earn what I get and to not ask for handouts like a street beggar. [posted by S. Y. Affolee on 5:02 AM : Monday, December 01, 2003  AIDS.org - Plenty of basic information. AIDS - Official Journal of the International AIDS Society. UNAIDS - The Joint United Nations Programme on HIV/AIDS. Divisions of HIV/AIDS Prevention - on the CDC website. The Body - An AIDS and HIV information resource. Induction of APOBEC3G ubiquitination and degradation by an HIV-1 Vif-Cul5-SCF complex. This is a very interesting paper on HIV that appeared in the journal Science in November. For the non-technical minded, a group at Johns Hopkins University characterized the function of the viral protein Vif. This targets the mammalian antiviral pathway by interacting with a couple of proteins to form a complex. The resulting "Vif-Cul5-SCF" complex tags the protein APOBEC3G (which is involved in the antiviral pathway) for degradation so as a result, there is a complete block of the host pathway for clearing a viral infection. (Edited at 8:00 PM - Yeah, I know this is way late, but my mind is totally not working today. And better late than never.) [posted by S. Y. Affolee on 6:23 AM : So I spent most of yesterday in the southern half of the state. In the afternoon, I meandered through Elm Street which is supposedly the heart of downtown Manchester. I was surprised that it was so empty--one would think people would be up and about doing some manic shopping sprees. In the evening, I went to one of the Thank God It's Over parties for NaNoWriMo which was held at a participant's house in Hudson. Very fun. I think the worst part was the traveling bit. I really don't like riding on buses, especially when I get motion sick. So even though I'm most likely going to do Nano again next year, I'm probably not going to any meetings/parties unless its within walking distance. [posted by S. Y. Affolee on 6:10 AM : |
