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Wednesday, February 28, 2007 The Extravagant Cocoon Snow can both be sublime and terrifying. Last weekend, I found myself carpooling with two other students, heading north towards snow, fog, and the Selkirk Mountains--some sixty miles south of the Canadian border. One could have been sensible and holed up at home to wait the bad weather out, but sensible was definitely out of the question when academics were involved. A memorable five mile stretch somewhere in the vicinity of Algoma kick-started the third hour of the trip--not because the scenery was particularly spectacular or interesting but because we couldn't see any scenery, let alone the road. The world had narrowed into nothing but snow, darkness, and the timid growling of the car heater. The driver's knuckles glowed white. The passenger riding shotgun denied being scared. I kept peering out of the windows feeling exhausted, anxious, and out of sorts. The final leg of the journey climbed about five thousand feet, peppered with reckless deer and sharp, hairpin turns. Other vehicles passed ours, roaring up the snow-caked roads like Evel Knievel on steroids. The final destination sparkled and winked, a cloud of lights nestled within a steep black-blue mantle, a commercialized village cut off from the rest of the world by trees and altitude. A ditzy blonde greeted us to the land of the ski bunnies by messing up our reservations, twice. The next day (after a somewhat nervous morning of presenting my research), I didn't head off to the slopes. Instead, I rented a pair of snowshoes and literally dove (head first) into the pines, away from the screaming kids, the ski enthusiasts, and the red-faced yuppies with their expensive equipment. Snowshoeing around the mountain was a bit like wading through cotton candy in flip-flops, while bundled up like a mummy. But it wasn't a bad way to get around--just different. On foot, I admired firs and hemlocks and larch. Animal tracks dotted the surrounding snow and squirrels overhead chattered warnings to trespassers--i.e. me. About ten minutes into the hike, snow began to fall, silent and windless. What other way can one cozily imagine being encased inside a snow globe? In the late afternoon, I stumbled into a nearby lodge after my exertions and curled up on a bench next to the fireplace. Fog covered the mountain and the nearby trees as it continued to snow. Just outside the window, hot pools steamed and ruddy-jowled, middle-aged men sucked in their guts before lolling about in the water with their younger buxom girlfriends. Inside, a plump matron sipping cola read a Harlequin. Before I briefly dozed off, the idea that I didn't belong in this place drifted in my thoughts. Resorts were for moneyed clichés. Resorts were for rich men and posh women who wouldn't think twice about paying ten bucks for a sandwich that would only cost three on a campus cafeteria. Resorts were for skiers and snowboarders who wanted to play with their lavish toys. They didn't care about their surroundings--only the flash they generated as they tackled yet another physical challenge. Around the resort, large expensive houses cut into the mountainside. Even in what was supposed to be wilderness, some people felt it necessary to mark the landscape with their conspicuous consumption. Or maybe I just don't quite understand all of this faux-survivalist luxury. Coming back, we passed Lake Pend Oreille. In the morning light, I saw the edges of the lake white with ice. Lonely figures sat on stools--small, black, ant-like--and fished at that precarious edge without a care in the world. [posted by S. Y. Affolee on 7:21 AM : Tuesday, February 27, 2007 Two Links Science vs Faith. (via Rhosgobel) Just one comment from me: "Heh." Married housekeepers are happier than footloose-and-fancy-free college girls. (via 2Blowhards) By their reasoning, they would say that I'm unhappy. Or at least less happy than my married counterparts. But you know, if someone is supposedly happier than I am, then good for them. I don't let that particularly worry me. My current philosophy about happiness is that you won't know what happiness is if you're not unhappy occasionally. (Although a rather snide voice in my head remarks, maybe married people might just use this study to justify their personal choices.) [posted by S. Y. Affolee on 6:45 PM : Thursday, February 22, 2007 Kids Who Lie To Their Parents An overheard call from an undergrad to his parent while coming back to lab from lunch: "No, it's a bad idea to come here this weekend. There's a jazz festival here this week, the largest in the nation. And the campus is packed with people." There's certainly a jazz festival here this week, but the last day is tomorrow. And even with the festival going on, the traffic on campus looks normal. [posted by S. Y. Affolee on 1:44 PM : The Thursday Threesome: Coffee in my Lap Onesome: Coffee--? ...or no? Black? Starbucks Cinnamon Dolce? Homeground beans (that you roasted)? Tea? Green? No? Water? What is your "sip of choice" right now? Water Twosome: "In my-- wildest dreams there's no way I would ever even consider _______!" You know, there's this saying: Never say never. Threesome: Lap--top or desktop? Which is your choice for hanging around on the net? ...or your choice if you had one? Laptop. Mobility is a big thing, you know. [posted by S. Y. Affolee on 11:51 AM : Wednesday, February 21, 2007 Very Brief Book Reviews: Part III Finally, I'm caught up. Two of the three books below (Greene and Sobel) are actually audiobooks. I got tired of listening to podcasts and decided to load up the iPod with audiobooks for the last three day weekend. They provided a nice distraction on some otherwise tedious days working in an empty lab with nothing but loud voices, arguing over the merits (or lack thereof) of RT-PCR, drifting in from the lab next door. Secrets of Saffron  by Pat Willard - First notice that this is a non-fiction book, not fiction. Books with facts in them usually get a lot of leeway even if they're deathly dull. But this is one of the rare instances in which the author's voice intrudes to the point that I wanted to tear out the pages in long, agonizing rips before throwing the damn thing out the window. The only thing preventing me from doing this is that I had no wish to damage library property. Talking about the history and culture of saffron is all well and good (the addition of recipes don't hurt either), but I don't want to hear about the author's failed love relationships or other episodes in her personal life that have minimal, if any, relevance to the topic on hand.The Fabric of the Cosmos by Brian Greene - Since I've read The Elegant Universe, this one seemed almost like deja vu because the two books are so complimentary to each other. There's a nice historical progression of how the concept of space evolved--from Newton to Einstein to now--as well as some interesting thoughts on quantum entanglement and the current state of superstring theory. In contrast to the above review, Greene only inserts himself where appropriate and his prose is both accessible and non-intrusive.The Planets by Dava Sobel - Take a tour from Mercury to Pluto with plenty of interesting detours to the history behind the planets' discoveries, the mythologies weaved by the ancients about these heavenly bodies, culture ranging from calendars to classical music, and even scientific controversy. There's nothing particularly new to learn in this book if you've kept up with science news and know a bit about the history of science, but it was a pleasing diversion nonetheless.[posted by S. Y. Affolee on 9:55 PM : Tuesday, February 20, 2007 Very Brief Book Reviews: Part II One of these days, I'm going to get burned out on urban paranormals. Most of them have very similar plot lines: vampire and/or shape-shifting protagonists struggle against antagonists of Great Evil, protagonists eventually win and live happily ever after with a liberal sprinkling of "sequel baiting" (i.e. the appearance of secondary characters who are "getting their own book" in the next entry of the series). But just because I'm still reading this genre doesn't mean that I read all of them indiscriminately. There are plenty of books in which I've read two or three chapters and then chucked because the author's writing style grated on my nerves. Warning: All of the following books are parts of series. I generally don't like reading series unless each volume can stand alone. Or I get hooked into it from the beginning. Bite Me If You Can by Lynsay Sands - On her way home, Leigh gets bitten by a rogue vampire and must be nursed back to health and tutored about the ways of the immortals by the hunter of rogue vampires, Lucian Argeneau. Yes, this sounds like just another one of those generic vampire books, but come on, this is Lynsay Sands. She does funny vampires--badass vampires stuck in completely ordinary situations like cleaning house and shopping at the mall. It was an amusing read until approximately ninety pages from the end when everything went downhill--mostly due to the completely unbelievable villain. This is the sixth book in the series, but all the books are standalone--so I don't think you'd be missing anything if you skip this entry.She's No Faerie Princess by Christine Warren - This is the second book in Warren's Other series--but it might as well be a singular novel since its connection to the previous one is tenuous at best. The niece of the queen of the faeries decides to take a little "vacation" by traveling to one of the fae's banned destinations: the human world--more specifically, Manhattan. But before she's barely out of the gate, she gets attacked by a demon and rescued by a grumpy, sleep-deprived werewolf trying to keep the peace between humans and paranormal beings. Of course, the appearance of the demon is an immediate sign that something larger and more sinister is at play. Although the identity of the bad guy is screamingly obvious and the volatile relationship between the two leads can get a bit annoying--this was a fun read; a no-brainer.Protector of the Flight by Robin D. Owens - While recuperating from a serious injury and escaping from the emotional rejection of her father, Calli Torcher stumbles through a portal to another world. But this is no accident--she's been Summoned to bond with flying horses called volarans and to fight a great evil encroaching onto the land. Through navigating her way through this new world, she finds acceptance when there was none in her old home. If it wasn't for the two previous books in this series (which is epic fantasy, not paranormal), I would have never picked this book up. I generally find horses, wings or not, boring. The volarans in Protector of the Flight weren't particularly original either. I was far more interested in the inner turmoil and character development of the main protagonist which I think the author pulled off satisfactorily. As for the main conflict overarching the series, Owens wimped out on this latest episode of the struggle against a still unknown enemy. It's already book three (and from what I can tell, there will be a total of six books)--where are the hints on why the evil is targeting that world anyway?Slave to Sensation by Nalini Singh - Yay! I found a new author who is a fun read and not a writer who makes me want to tear my hair out (cough like the author who gave the cover quote cough). Another surprising thing about Slave to Sensation is that there is a fair amount of solid world building here (compared to most other novels in the genre in which it's wishy-washy at best). In the future, humanity has been split into three branches--normal humans, changelings (humans who can shape-shift into animals), and the Psy--humans with impressive mental powers but no emotion. Sascha Duncan is Psy, but unlike others of her kind, she struggles to hide her emotions so she won't be turned in for "rehabilitation," i.e. turned into a vegetable. It was fun seeing the protagonist grapple with what she perceived as a flaw and come to realize that it may be one of her greater strengths.[posted by S. Y. Affolee on 8:59 PM : Monday, February 19, 2007 Very Brief Book Reviews: Part I The books are piling up and my memory is starting to go fuzzy on plot lines and such so I'm going to give the quick and dirty for each book in about a sentence (hopefully). Nabokov's Blues by Kurt Johnson and Steve Coates - This took me a little while to get through because it's about a subject that I know very little about (I majored in biology, but all my classes were molecular in nature)--butterfly taxonomy. I really could care less about insect genitalia since my bias towards any sort of classification is more towards genomic comparisons rather than painstaking morphological scrutiny, but I think the authors have succeeded in making what might have been a coma-inducing subject interesting. The highlight: an action-packed account of one of Johnson's colleagues dodging guerrillas in Central America just to bag some elusive and rare butterflies. Best New Paranormal Romance edited by Paula Guran - As I've mentioned in a previous post, the title of this new speculative fiction anthology garnered a bit of controversy--especially among rabid romance genre fans--because "paranormal romance" apparently means different things to different people. I'd say: disregard the title. The stories that stuck in my mind were either the funny ones (Delia Sherman's Walpurgis Afternoon, Heather Shaw's Single White Farmhouse, Sarah Prineas's A Treatise on Fewmets) or the ones that had some interesting use of language (Elizabeth Bear's Follow Me Light, Elizabeth Hand's Calypso in Berlin). Although BNPR is probably not going to supplant my fan-ish enthusiasm for YBFH, it's overall a promising start to a new anthology series. I'd definitely check out the next one. (Aside: Bear and Sherman's stories also appear in the 19th edition of YBFH. I first read Hand's story on SciFiction, a mag edited by one of the editors of YBFH.)White Lies by Jayne Ann Krentz - If you haven't noticed from my bookrolling list by now, Krentz (along with her pseudonyms Amanda Quick and Jayne Castle) is pretty much the only author in which I consistently pick up her new releases (I ignore the reprints since I don't particularly like anything that Krentz has written before 1990). I only read it for the dialogue between the main leads because it's quirky, amusing, and sometimes self-aware. As for the plot, for some reason it reminds me a lot of Krentz's flower trilogy she wrote under the Castle name. It's an okay read although I think her previous contemporary novel, All Night Long, had better suspense.Biophysical Studies of Retinal Proteins edited by Thomas Ebrey et al. - This is not so much a book as a bunch of scientific papers bound in book form. I was reading this because I was doing a bit of background research for a class presentation. Most sane people would just look up the info they needed and then return the tome back to the library, but I ended up reading the entire thing during my lunch breaks. In some ways, it is dull reading, but I found it intriguing on a historical level in how people went about dissecting the protein involved in vision processes.[posted by S. Y. Affolee on 11:20 PM : Friday, February 16, 2007 An Eventful Morning Coming back to lab, around 8 AM. I'm sweaty,grimy and covered with manure. But I have my samples. Fellow Grad Student: You don't look so good. Me: Yeah, well I had to wrestle some cows. They were being uncooperative. [posted by S. Y. Affolee on 5:48 PM : Thursday, February 15, 2007 The Thursday Threesome: Cups and Saucers Onesome: Cups-- and quarts? Can you remember the conversions for cooking or do you have to look them up? ...or do you just use the old "this much plus a little" method? I remember some conversions. The ones that matter anyway. Not that I actually measure anything--I approximate a lot of things when cooking. Twosome: and-- how did Valentine's Day go? Do you have a chocolate hangover today? Er, no. I have exam hangover. Threesome: Saucers-- of milk for the kittens? A pint of ice cream for you? Who gets the last snack of the night at your place? Me. [posted by S. Y. Affolee on 5:14 PM : Wednesday, February 14, 2007 Tangled Bank #73 Head on over to Lab Cat to read the latest in science blogging around the web in a special holiday edition. [posted by S. Y. Affolee on 7:24 AM : Monday, February 12, 2007 Belated The Thursday Threesome:Pitch, Yaw, and Roll Onesome: Pitch-- What is your singing range? ...and do you sing at all? Laurie, you're leading off here! I had one of my former cello teachers tell me that I had perfect pitch--but that's because I can tell when things (or people) are out of tune. As for me singing? I don't think so. Twosome: Yaw--'ll ken that one? Do you have any 'dialect words' that you use as a matter of course? "Ken", meaning "to understand" (Scottish and other derivations) in this case... No. Threesome: and Roll-- on down the road? Hey, if the roads were as icy as they've been in the Midwest and East would driving to work even be a consideration for you? Maybe--if walking to work would be worse. I can't depend on public transportation because the buses don't come past where I live. This reminds me of my drive down to Lewiston (Idaho for those of you not in the know) last Saturday. It was the first time I drove to that city since moving here and I'd forgotten that the place is buried in a crevasse in the mountains. The recent rains had washed pretty much all the snow and ice away but it was still foggy in the upper altitudes. And the steep grade down into city proper half freaked me out. I would so not drive there if the weather had been bad. Tangled Bank #72. I totally forgot to post this at the end of January, but go and read some cool science linkage. [posted by S. Y. Affolee on 6:26 PM : Friday, February 09, 2007 Yes, Another Link Outbreak! "An interactive teaching tool for use by students and science educators. Players must use microbial identification techniques to identify the causative agent of an illness outbreak." It's almost like Oregon Trail for micro geeks. [posted by S. Y. Affolee on 7:31 PM : Thursday, February 08, 2007 For the Arty Bacterial Fractals. Amazing what you can do with just a petri dish. I know, I know, another brief link. But there will definitely be something more substantial tomorrow. [posted by S. Y. Affolee on 5:50 PM : Wednesday, February 07, 2007 Science Writing Over at Adventures in Ethics and Science, there are a couple of posts about learning to write like a scientist. Those are some interesting questions which made me think about how I learned to write. Well, to be honest, I think I'm still learning how to write. One key to writing well is to read. A lot. Both bad and good papers have their uses--you can always use the good ones as models or guidelines to your own writing, and the bad ones can be examples of what not to do. I've written mock grant proposals before, but the whole process felt more like being thrown to the four winds with little feedback and even less guidance. If only someone actually offered a class that was solely focused on grant and/or journal article writing! My formal writing training, to say the least, is a bit spotty. I took several writing classes as an undergraduate but they were for fiction. (And fiction writing, even if it's speculative fiction, is very different from technical writing.) There was one science writing class that I took--to write for the lay person--but my views on that particular class were somewhat mixed. It was good that I had two people to look over my work: a technical writer/editor and a scientist who was an expert in the subject I chose writing in. But once again, guidance on how to write--particularly in a clear style--was a bit hit-or-miss. I find science blogging to be a self-imposed writing exercise. But even if everyone can read what I'm writing, I have no idea whether or not I'm writing well or perpetuating bad habits. On a blog, feedback for writing style is pretty much nonexistent or unreliable if you rely on blog directories with "ranking" systems. [posted by S. Y. Affolee on 5:48 PM : Tuesday, February 06, 2007 Questioning Species On the surface, the definition for a species seems relatively straightforward. According to the Linnaean classification scheme, species means the most specific group. It consists of individual organisms which share similar characteristics, genetics, and are able to interbreed. But what about those organisms--like bacteria--that can swap genes at will, not only within species but between species? Does the definition of "species" as we know it still hold or is a bit of redefinition in order? About a week and a half ago, I attended a seminar given by Claire M. Fraser-Liggett, the current president and lead investigator of The Institute of Genomic Research (TIGR). Fraser gave a talk about the impact of microbial genomics on the definition of microbial species that really challenged the entire concept of a species boundary. Although one wouldn't say that the bacterial mélange could possibly be lumped into one huge category, the promiscuous and fluid habits of microbes certainly make any attempt at definitive classification terribly difficult and complex. Descriptions of bacteria began in the late 19th century, focusing mainly on gross and easily observable characteristics like morphology, physiology and ecology. It was only in the latter half of the 20th century that molecular approaches began to be used to classify microbes. In today's era, microbial taxonomy rests mainly on comparing the sequences of the gene for the 16s ribosomal RNA. But not only is sequencing one gene--or even a handful of genes--rather limiting, but there's also an arbitrary cut-off point for saying which sequences are similar or not similar. Who's to say what a species is or isn't based on purely artificial parameters? Comparing sequences isn't the only problem. Other limits hamper current taxonomy as well. There are conflicts with phenotypic and phylogenetic information. Even within a species, bacteria do not exhibit the same phenotype. Metabolic reconstructions straight from the genome don't correlate with laboratory observations. And there isn't any good way to classify the bacteria that can't be grown by current culturing techniques let alone microbes that are nonculturable. One approach that Fraser-Liggett and her team at TIGR is pursuing is that of strain sequencing. The goal was to sequence many strains, all of which are considered to belong to one species of bacteria, to compile a core set of genes that would belong to all strains and characterize a given species. The results, to say the least, question even the notion that a set of genes could be used to define a species. For example, if one compared three different strains of Escherichia coli--the laboratory strain K-12, an uropathic strain, and O157:H7 (the strain that has caused many outbreaks that have gotten into recent news)--they share less than 40% of the genes. Now if you compare that to the statistic that we humans share more than 98% of our genes with chimps, you'd have to start to worry what we can call a microbial species. Lateral gene transfer and bacterial promiscuity aside, this gives rise to what Fraser-Liggett calls the "pan-genome" or a complete repertoire of genes that is associated with a species. This new term embraces the notion that there is significant genome diversity within a species. Not only is there a core set of genes belonging to all members of a species but there is a genetic "halo" of genes which belong to the set of genes for the species as a whole but actually is only strain specific. With these ideas in mind, there are perhaps two directions in which microbial taxonomy may take. One is the theory based model in which the notion of "species" is based on the mechanisms of speciation. The second is an operational based model in which species are defined as clusters or organisms that share common features. Unfortunately, the second model merely assumes that there are, in fact, species in the first place. [posted by S. Y. Affolee on 4:35 PM : Monday, February 05, 2007 Oldie But Goodie Bubble Chamber. A really cool simulation of what goes on in a bubble chamber. You can even make it into some nifty wallpaper! *Forgive me for posting such a brief link as my first entry for the science blogger challenge. I know. Lame. If you've noticed the timestamp, I just got out of TAing a class for most of the day. And I feel totally drained. (Before you get suspicious, it's a lab class. With lots of sections.) I'll have better stuff tomorrow, I promise. [posted by S. Y. Affolee on 8:35 PM : Saturday, February 03, 2007 Weekend Gibberish I went grocery shopping late this afternoon and the parking lots were packed. The store itself was a mad zoo with pretty much every aisle and every cashier occupied. One risks getting run over by either cars or shopping carts just to get a bunch of bananas. I first wondered if everyone was stockpiling because of a snow storm (I very rarely check up on the weather reports). But then realization dawned: tomorrow is the stupid superbowl. I don't give a damn about sports, but at least this evening, I've got the lab to myself... [posted by S. Y. Affolee on 6:10 PM : Thursday, February 01, 2007 The Thursday Threesome: Slicing and Dicing Onesome: Slicing-- your way through the fairways of life? Terrible metaphor, -eh? Do you have metaphor or simile that just drives you bonkers when you hear it? People should stop saying "chaps my ass." Not only does this sound stupid, but it gives me gross mental pictures. Twosome: and-- on and on and on. What's the duration of your 'long' phone calls? You know, the ones where you just chat and chat and chat? Guys, you may be able to pull an exemption on this one... Er, maybe half an hour. I'm not a guy, but I'm not the most talkative of people either. Threesome: dicing-- up anything for the game this weekend? ...or are you taking advantage of the sales? ...or is it a case of "what game?" I'm in the "what game?" group. See, I'm a student with no life. This weekend I will be stressing about upcoming, er, stuff. Even if I wanted to see a game or go sale-crazy, I couldn't. [posted by S. Y. Affolee on 7:06 AM : |
