Due to a comment I made in my previous post, I've been accused of having no fun because I have a stick up my ass. Thank you for the reprimand, but it won't prevent me from making similar comments in the future.
1. If you were to make a movie of your favorite character(s) in a book series...what actor(s) would you choose to play them, and why?
I am not one of those people who has to visualize characters as Famous People. I'd like to think I have more imagination than that. I also don't particularly like reading books belonging to a series. When it comes to multiple books, I'm a commitment-phobe. So I'll have to dig back further to when I was a kid--I was really into Lloyd Alexander. He's the guy who wrote the Chronicles of Prydain, but The Black Cauldron was already made into a movie. So I'll go with his Adventure series starring Vesper Holly, a sort of female Indiana Jones. Vesper is nothing like Laura Croft in Tomb Raider so I'd have to pick someone like Meg Ryan.
2. If you were to make a movie of your favorite blog author (based on what you read there), what actor/actress would you choose to play that author? (you may choose more than one if you like)
Hm. I don't have a favorite blog author, but here are two that I came up with off the top of my head.
Dustbury - Jack Nicholson (as I've posted in his comments) Pharyngula - Harrison Ford (with a beard)
It's actually sort of hard trying to pair up an actor/actress with a blogger--I mean, a blogger is so individual and representing them with someone who can only pretend to be them seems so insipid.
After many, many months of saying so, I've finally finished Waking the Moon by Elizabeth Hand. I wasn't kidding when I mentioned in a previous post that the rich prose can put you into a coma if you ingest too much of it at once. If you're a speed reader, you can disregard my warnings. Otherwise--well, the only other book I can sort of compare it to is Neil Gaiman's American Gods, but even that is somewhat shaped by circumstance. True, both novels are dark and concern themselves with pagan deities, but I started both with the preconception that they might make for light plane ride reading. I ended up wishing I had been more careful in picking up something less serious.
We first meet the protagonist of Waking the Moon, Katherine Sweeney Cassidy, in her first semester at the University of the Archangels and Saint John the Divine in Washington, D.C. She feels completely out of place in the rarefied atmosphere of academics and privileged kids until she is befriended by Oliver and Angelica, two strangely beautiful students with an even stranger destiny. Amidst the typical college antics of partying and drugs, Sweeney glimpses a horrible fantastic underworld exerting its pull on her friends. Her first semester is cut short by a terrible accident and for the next twenty years, she sinks into an emotional coma until she is given a second chance at the cusp of a possible revolution.
With all the vivid and fantastic imagery, it wouldn't be any stretch to call it an erotic horror-fantasy, but it would be short-changing it to say it's only sex and death. The central conflict is between a secret patriarchal society called the Benandanti and the resurgence of a cult demanding blood sacrifices to its moon goddess. Who is right? As Sweeney points out, neither. Extremism on any side, be it the patronizing old boy's network or militant feminism, is repugnant. And as this theme suggests, it would be a mistake not to take the novel seriously and thoughtfully.
Onto a lighter note, I've also finished A Scholar of Magics by Caroline Stevermer. One could say that this is a sequel to A College of Magics but it can stand quite well alone. (Aside: I found A College of Magics as adult fiction several years ago, but A Scholar of Magics is--surprise--marketed as "young adult." The level of writing between the two novels isn't different, but I had a heck of a time trying to track down the sequel at the local bookstore.) It's the early 1900s and Samuel Lambert, sharpshooter for Kiowa Bob's Wild West Show, has been invited to Glasscastle University to lend his talents to the top secret Agincourt Project. Glasscastle is like the typical British college with its snobbish dons and students and stunning architecture, but in some ways more dangerous because magic is taught there. All Lambert has to worry about is tea with the provost's wife until the provost's sister Jane Brailsford unexpectedly drops in for a visit.
A Scholar of Magics is a light-hearted magical adventure set in the very proper Edwardian England and the effect is quite original and amusing. Lambert is an easy going young man longing to study magic at Glasscastle despite the fact that he has the wrong background to be admitted as a student. Jane is a teacher at a girl's college of magic in France who loves to drive motor cars at breakneck speed. As the reader follows Lambert and Jane as they chase down henchmen in bowler hats, an absent-minded don refusing to take up his post as the Warden of the West, and a mysterious weapon, the magic is actually worked in quite subtly and tastefully. Like one of the dons of Glasscastle might say, the magic follows a certain logic whose study can be approached like science.
Unlike Waking the Moon, Stevermer's novel is good clean fantasy (perhaps this is the reason it's been shelved as young adult). There is not that much violence considering the main character's proficiency with firearms. There isn't even any kissing despite the romantic subplot. But this is only proof that a story doesn't necessarily need disturbing elements to make it an interesting story. I thoroughly enjoyed digging into A Scholar of Magics--it was like reading Agatha Christie if she wrote humorous fantasy instead of mystery.
Legends are tricky things. Some of them have so many versions that one wonders if one of them was really passed down through the years or someone just made it up on the spot. The Chinese legend about the discovery of the silkworm is one such story. Was it discovered by an ancient empress named Lei Zu as she took an afternoon walk? Was it the Huang Di when he observed a silkworm cocoon dropping into his tea? Or was it Xi Lingshi, a Chinese princess who lived five thousand years ago? Nonetheless the silkworm Bombyx mori has been the center of sericulture for a very long time.
Silkworms also have the distinction of being the only domesticated insect to date. B. mori is entirely dependent on humans for survival as they have lost the ability for flight. Aside from the silk industry, silkworms have also been useful for basic research and biotechnology--particularly on the study of pheromones.
Certainly, Bombyx mori has been one of those fringe model organisms--at least to my thinking. Even as an invertebrate, it doesn't hold the same cachet as Caenorhabditis elegans or Drosophila melanogaster. To put it bluntly, it doesn't have nearly as much scientific precedence as the worm and the fly. No one has ever followed the silkworm cell lineages from egg to adult. No one looked for white eyed mutants in a colony of silkworms. But maybe today, it's slowly changing.
But why use B. mori at all? Well, for one thing, it's easy to breed. People have been doing it for thousands of years after all. Generation time is definitely faster than that of a mouse (and they probably cost less to house too). And I'm pretty sure no animal rights activist would break into a lab to free all the silkworms.
In a recent issue of Molecular Microbiology, Kaito et al. have taken the silkworm and put it to a quite different use--as an infection model. Most scientists are more familiar with the mouse, worm, and fly as models for pathogen-host interaction and in a way it's easier to examine how a pathogen infects a host using those organisms because their genetics are more understood. But mice are expensive and worms and flies--compared to the silkworm--are too tiny to work with easily.
To test if the silkworm could be used as an infection model, the researchers injected silkworm larvae with Staphylococcus aureus and a staph mutant for a known virulence gene. The larvae injected with the wildtype staph died off much faster than the larvae injected with the mutant staph--a strong indication that the silkworm could be used as a model. But the real test was, could they use the silkworm to identify new virulence genes in staph?
Staph has over 500 genes whose functions are still not known. In order to search for virulence genes among those unknown genes, Kaito et al. constructed staph mutants for 100 of those genes and injected these mutants into silkworms. Only three batches of silkworms survived--those that were injected with the staph mutants of the cvf (conserved virulence factor) genes. Two of these genes were confirmed to affect staph's virulence by injecting these into mice. The cvf genes were later found to control the bacteria's production of toxins.
So the results look promising. But will the silkworm ever be the new laboratory mouse? It's certainly an interesting model that has some advantages, but I would think not. There are vast differences between invertebrates and mammals, and rodents (and monkeys) are currently still the best models we have for human disease. Sure, virulence genes can be pulled out by using the silkworm--but there will always be false positives while other genes might be missed entirely. It would make sense that a bacterium would use different weapons if it finds itself in a silkworm or a human.
Seems like a lot of people are quite fond of that line. I once sat through a seminar entitled "Sex, Lies and Videotape" which was about Drosophila courtship behavior (and yes, there were videos shown of flies doing it). Interesting research, but the speaker was very boring.
Onesome: Sex...When did you learn about sex? Was it through those films at school? Word of Mouth? Your parents?
When I was a kid, I devoured books and among those that I went through with more frequency than most were science books. (I suppose it isn't any different now.) My parents never really sat me down and told me about "the birds and the bees"--I don't recall having any such discussion with them. I remember reading about human reproduction although I no longer remember what the title or who the author was. It was all very clinical and at the time I didn't realize that some people would consider it a Very Big Deal.
Twosome: ...Lies-- ...do you believe little white lies are all around us? Or do you prefer only the truth even if it hurts someone's feelings?
I prefer the truth. The only exception is when someone asks me "How are you doing?" and clearly they are only doing this as a greeting. So instead of launching into a long-winded complaint of how my life sucks, I just say, "I'm fine."
Threesome: and Videotape-- ...do you buy movies on Video and/or DVD? Or do you prefer to rent? What kind of movies do you add to your collection?
A World of Pain. (via Boing Boing) A prof tries to scare a thief into giving back his laptop. So far, it hasn't worked.
Of Course Macs Are More Expensive...Aren't They? An interesting article on how to compare the specs between Macs and PCs. I think it's all a matter of need. I can deal with a stripped down computer without all the "bells and whistles". I'm no computer geek in need of a lot of processing power to play games. All I really need is a word processor and connection to the internet. And I'd imagine most people are like that too.
Last night, I breezed through a short novel titled Sorcery & Cecelia written by Patricia C. Wrede and Caroline Stevermer. It's really a shame that this book (and others like it) are being marketed solely to "young adults." Sorcery & Cecelia is quite an amusing fantasy piece but somehow, I doubt the audience would be anyone but twelve year olds. How many adults do you ever notice perusing the young adult fiction shelf? None, with the exception of overbearing mothers who want to control their offspring's literary intake. Even the publishers of the wildly successful Harry Potter series had to reprint the books in adult editions in an attempt to get more adult readers.
(Aside: Of course, I'm not ashamed to read anything. Only the marketers have the bad taste of putting bad covers and pigeonholing manuscripts which deserve no such thing.)
Sorcery & Cecelia was originally conceived by the two authors as a letter writing game with each author writing a letter in character but not revealing to the other what plot she had in mind. The correspondence in this novel is between two cousins who are also friends--Cecelia and Kate. After the "goat incident", Kate is sent off to London with another cousin and aunt to attend a Season while Cecelia remains in the country. Despite the distance between the two of them, Kate and Cecelia manage to get into hot water anyway. Kate nearly gets poisoned by some hot chocolate from a magic chocolate pot meant for a mysterious marquis while Cecelia discovers a charm-bag underneath her brother's bed after she notices him acting strangely.
The authors describe it as Jane Austen inviting J.R.R. Tolkien for tea, but perhaps a better picture would be Regency England in an alternate universe. Cecelia and Kate's world is not at all surprised that there are wizards and enchantments running amuck. Perhaps with those of you with more high-brow fantasy tastes, the genre would fit squarely in that occupied by the far more verbose and ponderous Jonathan Strange & Mr. Norrell (which I have yet to finish, but I'm getting there).
Something about driving in the rain raises my hackles. More people than usual seem to have a death wish on the road, driving fast and reckless. They tailgate, even when I reach five miles over the speed limit. The slick grayness and the churning clouds overhead--is this what dares people to tread that line between here and oblivion? Is it because unlike their dull jobs and boring home lives, this is the only moment that they feel alive?
I must admit there's a certain beauty about rainy traffic. A car is not just a car--but a mechanical mermaid rising out of a silver mist--as the hind wheels kick up water. The roads are dark things curling intimately around dripping hills and buildings and budding trees. Perhaps the other drivers feel this too and subconsciously desire that morbid thought of running aground, skin upon cold wet pavement.
* * *
A book sale, how could I miss one? This one was held at a local high school, the books filling two gymnasiums. Why the school had two gymnasiums, I don't know--the high school I went to was larger than this school yet only had one gym. Patrons stuffed boxes and bags with books--it was half-price today--seemingly without any thought about what the books were about.
What makes a person pick up a book for consideration? Besides the author and the title, there is something said for typeface and color and cover art. For some reason, none of those things really caught my eye at the sale. There was too much popular fiction--the plot-driven and cardboard character action adventure kind--and not much of anything else. It's pretty bad when I say even Stephen King was almost non-existent.
As for non-fiction, it was mostly sociology and history and religion and cooking books. The only book I bought was one about the transcontinental railroad. I was somewhat disappointed, but there will be other book sales.
The relationship between good things and bad things is like the second law of thermodynamics. When bad things happen, it's really bad. When good things happen, something else bad will happen. Just as no matter how much order you put to things, things will naturally become disordered, packaging things in good will not stop all the bad things from spilling out and swamping everything.
Three steps forward and two steps back and all that drivel. For about ten minutes, I was glad that all my efforts for one thing wasn't for naught. And then I found out that my efforts for another thing was definitely for naught. Such is life, you may admonish me. But that doesn't mean I have to like it.
Onesome: Domain--Hypothetically, if you could own any domain name you wanted, what would it be and why?
The first thing that came to mind was noodle.com, but that was only because for some previous question about personalized license plates, I answered NOODLE.
Or maybe something with a color in it like purple.com--something simple and easy to remember, that's for sure, except I wouldn't really know what to do with it.
Twosome: Name-- Are you called by something other than your legal name? If not, have you ever had a nickname? Or done something weird with your name, to try and stand out? Like an odd spelling or a slightly different pronunciation? Or just flat out wanted to change your name? To what?
No. I don't have a nickname. I haven't done anything weird with my name (too short for that). My name is also way too short for weird spellings although different people have done different pronunciations without any prompting from me. I don't particularly want to change my name--at least it isn't too common (like Jennifer or Michelle or Grace or whatever Asian parents give their daughters).
Threesome: Renewal--Do you have any magazine or other subscription that is an absolute 'must renew' whenever you get the notice?
Head on over to Circadiana to read this week's compilation of science blogging. As always, excellent stuff to spend the week perusing and thinking about. Of course, this isn't just any edition of Tangled Bank, this marks the one year point of the weblog carnival. So a happy birthday to an internet meme that has survived, flourished, and succeeded!
I don't know about you, but this is one of the few memes out there that I actually learn something from. I've also discovered plenty of wonderful science bloggers who I wouldn't have found otherwise. No offense to those numerous political bloggers, journallers, and cat bloggers, but there is only so much one can take of vitrolic punditry, excessive introspection, and cute pictures. Sometimes one needs something different with substance.
I've been lucky to be one of the first people to be featured in the first edition of Tangled Bank as well as having the pleasure of hosting another edition. My original intent for submitting was not to get hits and readers (although that is quite nice) but to spur myself to write more science-oriented posts. I still don't post as many science articles as I'd like to, but compared to the period before the creation of the carnival, science blogging was at best, sporadic.
Science blogging is different than, well, the kind of blogging that most people do. I don't consider myself a complete obsessive, but I do enjoy doing background reading on a post I'm thinking about writing. And the added bonus is that I don't feel like I'm wasting too much time doing something unproductive--after all, I'm learning. I don't find this daunting because science is just plain fun. If it was any other type of niche blogging like finance or po-mo criticism, I might enjoy reading about it and learn something. But I wouldn't go so far as to blog about it because I don't personally find those subjects fun.
Is all blogging going toward one niche or another, just as people in the real world specialize to different jobs? General and personal blogging is easy to do--anyone can do it--and it doesn't take that long to type up something that everyone (or most everyone) can relate to. Sometimes I wonder, what's the challenge in that? (And sometimes there is the annoying thought that no one will take me seriously if I'm not serious all the time.) But I know I can't just give up general blogging--it's what I started with and I don't have the energy to niche blog every day.
How on earth did I manage to go from a meme announcement, a testamonial, and then navel gazing? Oh well, that's the nature of most weblogs and mine isn't any different.
*Today looks like such a nice day. It's a shame I'm stuck inside.
*I was reading an entry from Warrior of the Woods and I was remembering this one time that I took a bus trip to Boston and one of the passengers (a really chatty woman who I couldn't tune out even though I tried to take a nap) who said that she couldn't imagine not being a mother. She didn't have any kids and she was not pregnant. She didn't even have an SO. Yet she was planning to spend her life being a mother. That's nice and all, but there's more to life than just being a mother.
*Some people naturally go around with a slack jaw or mouth agape so their two front teeth poke out from underneath their top lip. I am not observing just one person. This is many people--people I know, people I just pass on the street or in stores, drivers whizzing by. People are a lot more like rabbits than we realize.
*I have to thank Pharyngula for submitting one of my entries for a weblog carnival called Smarter Than I. (Thank you!) I've been calling myself an idiot for the past couple of months (for various reasons) and it's nice to know that at least one person out there doesn't think I'm brain dead.
*Books Banned on Flights? Hopefully this is just a confusion between matchbooks and real books, but if not--we are in so much trouble. I always bring a kazillion books and papers with me on a flight and I'd really hate to think that someone believes that paper and ink are WMDs.
*Why is it that when someone asks me, "Can you smell that?" and refer to something bad like gas or stinking bacteria, I can hardly smell it, but when someone wears a lot of perfume and cologne, I can detect it several feet away?
*I saw the news about the new pope. I am not exactly impressed.
It was 1962 Berlin, and Heinz Stolp had just run out of membrane filters. Stolp was attempting to isolate bacteriophages that would kill plant pathogens by filtering various soil solutions and applying the filtrate to a lawn of bacteria in a petri dish. The filters had 0.2 micron pores which would let bacteriophage but not other larger particles (such as bacteria) through. If the filtrate contained bacteriophages, they would kill the bacteria if added to the petri dish. This can be observed by the plaques or zones of dead bacteria on the lawn. But Stolp had no more 0.2 micron filters so instead, he used a sintered glass filter which had pores as large as 1.35 microns.
The filtrate was layered on a lawn of Pseudomonas phaseolicola (a scourge of bean plants) and left to incubate overnight. The next day, Stolp didn't see any phage plaques on the bacterial lawns and concluded that that particular experiment didn't work. But instead of immediately throwing the plates away, he left them on his lab bench. Two days later, he happened to glance at the plates again and was surprised that this time, there were plaques.
The plaques were isolated and mixed into a solution that was layered on another lawn of bacteria. Again, the plaques didn't appear until two or three days later which really was strange behavior. Bacteriophages usually lyse bacteria by 24 hours. Stolp found the answer to this puzzle when he examined the plaque under a microscope: tiny, fast moving microbes were attacking and killing the larger Pseudomonas like a spray of bullets intent on making a messy end for its victim.
Stolp and his colleague Mortimer Starr also isolated these tiny predatory microbes from other soil samples and named them Bdellovibrio bacteriovorus (bdello: leech, vibrio: curved, bacteriovorus: bacteria eater). Later researchers discovered Bdellovibrio in a variety of environments--from the aquatic to the human--an indication that they are rather common, perhaps even in our guts. They're around 0.2-0.5 microns wide and 0.5-2.5 microns long, small enough to get through that glass filter. But culturing them is difficult. Unlike other bacteria, they cannot make their own food from the raw materials of conventional media. They depend on prey bacteria to survive.
Image: Max Planck Institute for Developmental Biology/Rendulic, Berger and Schuster
Considering their size, the Bdellovibrio are super swimmers, reaching up to 160 microns per second. During attack-phase, flagella whip into movement and guided by chemotaxis, Bdellovibrio "sniff out" nearby bacterial prey and torpedo themselves toward their victims. In the next stages, they collide with their prey, attach to the cell surface and enter the prey periplasm by boring a hole in the outer membrane of the prey, squeezing themselves through the opening, and resealing the pore. Once inside the periplasm, a Bdellovibrio multiplies and the prey becomes a bloated structure called the bdelloplast. And when all of the prey cytoplasm is consumed, the Bdellovibrio break out of the bdelloplast to seek more prey.
It's sort of like a microbe version of the movie Alien. Imagine the alien burrowing into your skin, eating your insides, and finally busting out of your spent shell by dissolving your skin. What a gruesome way to die.
One could almost feel sorry for the terrible fate that meet Bdellovibrio prey. Almost. See, Bdellovibrio primarily prey on bacteria that we consider pathogens. Not only do they prey on plant pathogenic Pseudomonas as Stolp observed but also other Pseudomonas species that infect burn wounds and the lungs of cystic fibrosis patients. Some other human pathogens that can become prey are E. coli, Salmonella, and Legionella. On the other hand, Bdellovibrio cannot grow in eukaryotic cells which makes them completely harmless to us.
Is it possible, then, that this may be a case of that old Arab proverb, "the enemy of my enemy is my friend"? Certainly the recent scientific literature seems headed that way. In Nature Reviews Microbiology, Sockett and Lambert discuss how Bdellovibrio may be used as a therapeutic agent. There are several reasons to recommend using this microbe as an antibiotic. Bdellovibrio can infiltrate biofilms, a protective matrix of polysaccharide some bacteria shield themselves with, that stubbornly cling to implanted devices like catheters. These microbes are also resistant to chemical antibiotics so they could be used in combination with drugs like penicillin to vigorously fight infection. And although Bdellovibrio contains lipopolysaccharide (LPS)--a potent stimulator of the immune response present in gram-negative bacteria--on its cell wall, the Bdellovibrio LPS is significantly different than other gram-negative LPS that it is unlikely that it would cause a severe reaction in the human immune system.
So just as we now use macroscopic blood-sucking leeches as FDA approved medical devices, these microscopic "leeches" may prove to be a "living antibiotic" as potent as a top-of-the-line chemical arsenal.
Some women love sales at the mall or department store. I hate shopping at those places. What I really love are book sales. And the great thing about chasing down book sales at out-of-the-way and little publicized places is that hardly anyone my age is doing this kind of stuff. I have the illusion that I'm doing something so cutting edge and cool that no one has caught on yet. Instead, they're all busy pushing buttons over at Amazon.
Or maybe I'm just a luddite.
Yesterday, I went to a senior center in Vermont. Normal college kiddies wouldn't be caught dead in a senior center. But for me, who the hell cares? They have books. Every single book was new, pristine, never before been read, just released. And you can't complain when all the hardbacks were four for ten bucks and the paperbacks three for a buck. Some books that I purchased: Collapse by Jared Diamond, Going Postal by Terry Pratchett, An Alchemy of Mind by Diane Ackerman, and (I was surprised I found this) No Plot? No Problem! by Nanowrimo founder Chris Baty.
Most of the other patrons at the book sale were either senior citizens or mothers with small kids. The small kids thought the whole affair very tedious and boring and ignored the books in favor of horseplay. The mothers pretty much cleared out all the children's books the first fifteen minutes I was there. There was one teenage boy who remained at the sci-fi/fantasy section and basically added more of those books to his own towering pile. As for the senior citizens: the old ladies fought over the cookbooks and romance novels while their husbands just puttered around looking rather bewildered. And I got the rest of the non-fiction all to myself. (Bwahahaha!)
I still feel totally behind on my reading. One of these days, I'm going to finish everything I own before I attempt to acquire any new books. Or at least sincerely try to. The last time I posted about my reading queue, I had mentioned that I was going to finish Waking the Moon by Elizabeth Hand before the month is out. I'm finally making some headway into the novel, but I'm reminded of the reason why I put it down in the first place--the imagery is so rich and hallucinatory it's like eating expensive chocolate and then going into a seizure. There are just some things one can't breeze through without being completely overloaded.
I'm also in the middle of Stephen Jay Gould's The Mismeasure of Man. Or maybe more accurately, just starting it. I have the revised and expanded edition so I had to slog through the rather lengthy "Introduction to the Revised and Expanded Edition" which I think, would have been better if I had read it last instead of first.
On a lighter (heavier?) note, I had checked out The Complete Cartoons of The New Yorker at the local library and I'm almost finished with it. The monster of a book probably weighs more than some kids. At least most of it is pictures.
The Ultimate Tree-Ring Pages. A dendrochronology site where the author has attempted to amass as much information as possible about the subject.
Foiling Spies at the Vatican. "Computer hackers, electronic bugs and supersensitive microphones threaten to pierce the Vatican's thick walls next week when cardinals gather in the Sistine Chapel to name a papal successor. Spying has gotten a lot more sophisticated since John Paul II was elected in 1978, but the Vatican seems confident it can protect the centuries-old tradition of secrecy that surrounds the gathering."
Un-brellas. Ratings of umbrellas. I say go for the cheepo umbrella (unless you're some sort of umbrella freak). I bought one for $1 three years ago and it still works.
The worst thing about driving around at sunset is that you can't see anything. Let me explain: the sun is fairly low so there's no glare and there's still some light in the sky so it looks sort of light bluish-grayish, washed out. Headlights are rather ineffective--they're useful for oncoming cars but as for seeing right in front of you? Nuh-uh.
There's this stretch of 120 going into Hanover, right after the hub with the interstate but before the medical center, that goes uphill into forest. During sunset, the forest is pretty much black and casts a shadow on the road so you can barely make out the shoulders. I hate this particular part of 120--the going uphill part--because everyone is trying to outrun everyone else before the two lanes merge at the top.
This evening, I was heading back to the college (lab stuff, blah, blah, blah) and as usual, I hit that uphill stretch. There are cars far behind and I'm going about 50 mph and I'm thinking, there's no way somebody's going to try to pass me. (I think the speed limit is 50 mph although I must admit, I haven't noticed any signs on that part of the road except on the opposite side going downhill where there's one warning drivers to reduce to 40 mph ahead.) But of course, somebody does pass me--an SUV--and it's flying. 70, 80 mph?
And then, once the SUV gets past me, it pulls in front and breaks. I'm thinking: WTF? I break and then I see flashing blue lights on the opposite side of the road where previously I've seen nothing but shadowy trees. Crap.
The police cruiser sweeps around and suddenly it's behind me. It felt somewhat surreal seeing all these blue lights in the rearview mirror and all the expletives streaming through my head. I so did not need a ticket right now (or ever) and I was trying to rack my brain to see if I had inadvertently broken some obscure traffic rule. I made to drive onto the shoulder, but then the cruiser passed me and pulled over the SUV.
I was somewhat numb and shaken, but before I could even breathe a sigh of relief, I saw red and white lights in the rearview mirror and this time I had to pull over for real to let a firetruck pass. When I was finally back on the road, my confidence in driving was pretty much wrecked. Even though the weather is clear, tonight is just a bad time to get behind the wheel.
What it all comes down to is: I don't want to be caught speeding. It's not so much about being afraid of breaking rules but about paying for the ticket. I mean, what if a cop pulls me over even when I'm not speeding or breaking any traffic rules just to get some ticket quota? How on earth am I going to contest that? Yeah, so the SUV deserved to be pulled over, but that doesn't mean I have to like authority figures.
Don't speed, send things in on time, clean up any messes I make so other people won't get annoyed. I will even do these things without somebody breathing down my neck. Preferably without anyone breathing down my neck. Some people don't see it that way--sometimes when I do something under their eyes that I would have done anyway were I alone, they praise me "Good girl! Good girl!" as if I would have otherwise behaved like a barbarian left to my own devices.
On an unrelated note: I think the saying "Good girl!" (or "Good boy!") should be banned in normal discourse. It makes people sound like they're talking to dogs and not other people.
Reef Check. "Founded in 1996, Reef Check is a volunteer, ocean conservation organization designed to save coral reefs globally and temperate reefs in California."
It's in the Blood! A documentary history of Linus Pauling, hemoglobin, and sickle cell anemia.
Bogus blogs snare fresh victims. "The bogus web journals are being used as traps that infect visitor's machines with keylogging software or viruses." Yes, but only if you're stupid enough to click on a link some unknown person e-mails or IMs you. Hopefully they won't get indexed by search engines...
Natural Nuclear Reactors. (via Kottke) It's all started by microbes with the ability to specifically concentrate uranium.
Oh, and I can't forget the Friday Ark. I am still wondering what's up with all those cat bloggers. Does owning a cat make one more likely to own a blog? Or does owning a cat make one more likely to post cat pictures on the web?
Murburg's behaviour bewilders scientists. Okay, so I'm way late in posting this, but this is fascinating stuff. The curious thing about this is that most of the victims have been young children which is not the same pattern as previous outbreaks.
National Library Week. Also late with this post, but as people always say, better late than never. Have you been to a library this week? I have, but unfortunately it was not for checking out books.
Little India. Pages of a children's book about Indian mythology. Cute.
Creative licence. "Kate Bulkley reports on an online initiative by broadcasters that will allow the public to experiment with archive material."
The Attending Sign. "Along with the emergency-department registration staff, the triage nurse, and the nursing student, they had already asked Mrs. J. if she was taking any new medications. Yet the patient waited to tell me—the attending E.R. doc and the final and most senior questioner—about her new antibiotics." Crazy patients. You're not doing anyone (most of all yourself) any good if you hold back any info to the medical staff.
More and More, Kids Say the Foulest Things. I'm not particularly offended by the swear words peppering normal conversation (yes, I'm pretty much desensitized to that), but I am annoyed. It's not really the coarseness of it that gets to me, but the sheer banality. It's boring and counterproductive and completely dilutes whatever message they're trying to get across. Try to say things without all those expletives and what you say will be more clear and powerful for it.
Transylvania, move over. You've got nothing on the real-life vampires in Spain.
Lake Estanya in northeastern Spain is a karstic lake, a watery sinkhole carved into limestone and rich in minerals such as sulfates. It's shaped like the figure "8" and is at most, 20 meters deep. The lake is extremely stratified: as the light transmitted through the water decreases with depth, anoxic conditions increase. The top purple layers are thick with phototrophic sulfur bacteria due to the abundant amounts of light and sulfide.
These purple sulfer bacteria are species of rod-shaped Chromatium characterized by their ability for anoygenic photosynthesis in which no oxygen is produced. Researchers anaylzing these bacteria noted that there were primarily three Chromatium species swimming around in the lake: C. okenii, C. minus, and C. vinosum. In cultures of these Chromatium species, they noticed that there were smaller bacteria attached to them.
As you increase in lake depth, less sunlight is available and Chromatium decreases viability. Surprisingly, as depth increased, so did the number of the smaller bacteria which in turn preyed on the weakened Chromatium. These small round bacteria or Vampirococci were so named because they attached to their prey through pilus structures and "sucked" it dry of cytoplasm. The Vampirococcus grows in anaerobic conditions and can only replicate while it's attached to the prey. And in the end, all that remains of the poor microbe victim after the Vampirococcus is done is the husk: the cell wall, cytoplasmic membrane, and maybe bits of leftover organelles.
Onesome:This--is pretty much the start of Spring (regardless of the snow in the east and midwest last week!); what's on your to-do list for the next few weeks to transition away from this long Winter we've been having?
All I can say is that things have been extremely stressful. My neighbors were quiet for once, but I've had a pretty rotten night's sleep. I went to bed at 10pm and woke up at 12am, 1am, 3am, and 4am. After 4am, I decided to get out of bed. I skipped breakfast and I'm still feeling too stressful to eat.
As for transitioning from winter to spring--I need to change my car's snow tires to summer tires sometime this month.
Twosome: Week's-- What is this week's reading assignment for you? Is there a new book on the night stand? (Students, we're not talking the Chem 104 book either < g >!)
I am also reading some papers that might make an interesting science post on the weblog.
Threesome: Feature--What feature would you like to have on your web site that you currently don't have? ...or is there something you do have that you'd like dialed in just a little bit better? Just curious...
I like to keep this website relatively simple. The last major things I added was an atom feed and a page linking to all my science posts. I'm sure it would be easier if I was using one of those other weblog services that provided sorting by subject, but frankly, I don't think anyone would use it (or should for that matter). To really get the gist of a weblog, one should read it in chronological order.
Other things I don't particularly need or am too lazy to install: trackbacks (not enough people link back to me to make this worthwhile), separate pages for each post (too many pages to maintain), blogroll on front page (makes things too cluttered), and a "read more" link (my posts aren't that long).
Dr. Johnson on These Girls These Days. Middle-aged guy thinks young women these days are shallow. Yawn. What's new? Old people always think younger people are shallow. However, I'm not even going to try putting myself up as an exception. I'm sure someone somewhere thinks I'm shallow.
Evil Overlord List. I think the main things to do as a sensible evil overlord are: treat your henchmen/minions well so they don't turn on you, listen to common sense and your advisors so you don't do anything stupid, and nip any trouble in the bud before things get out of hand.
Animal laughs no joke says expert. "Although no one has investigated the possibility of rat humour, if it exists, it is likely to be heavily laced with slapstick."
Last Saturday, I attended a Midori concert (yes, I said I would post yesterday, but I got sidetracked by various things) which I thought quite cool. Was it cool because I got to hear a Famous Person play? Undoubtedly. I found it interesting that she was able to pull off several different styles in one performance--to see the program notes that Midori wrote herself see here (pdf).
Sitting in the auditorium before the concert was somewhat odd. The backstage of the HOP is not soundproofed so I was able to hear Midori and the pianist Robert McDonald (who has accompanied her for about 17 years) warming up. Then again, I was fairly close to the stage--second row, center--a great seat--close enough to see the reflection of the first row on the Steinway, courtesy from non-procrastination when tickets to the concert went on sale. And as usual, the audience was a mixture of old snooty people (alumni?), college profs in tweed, and grungy college students. (Just so you know, I did not go to the concert looking grungy--being flagrantly rebellious of expected attire at classical concerts is so passé.)
Midori was shorter than I had imagined or perhaps this was the result of my preconception that all violinists appear statuesque on stage. At any rate, I couldn't help do one of those comparisons with the piano and violin--like a semi to a Miata. The problem with being a pianist is that you're sitting on a bench and you're showing the audience only one side. As a violinist, you're standing and you're free to move. Midori took advantage of this and literally glittered (she was wearing a shiny gold dress) as she performed.
At a question and answer session after the concert, Midori said that she liked all of the pieces because she got to play in different styles but my favorite was the third movement (Andante) of J.S. Bach's Sonata No. 2 in A Minor, BWV 1003. This was solo violin so none of the tone was muddied up by a background piano, but with all the double stops, it sounded like more than one violin playing. At that particular moment, it was as if Bach had been distilled into a pure Zen-like soundscape.
One question asked by the audience was--why did she have her eyes closed while she was playing? Actually, she didn't have her eyes closed. She was looking down at the bridge and fingerboard of her violin and to the audience, it appeared that she had her eyes closed. Anyways, it had the effect that she was concentrating on the music and the audience itself happened to be there to hear her play by coincidence.
How to describe Midori's style? "Light" would be the wrong word. I'd say her passion for the music is more easy-going and loose. Sure, she can be ferocious when the music calls for it, but unlike other violinists who grind away with sweat pouring down their temples, she goes with the flow letting each note speak instead of channeling them down some preconceived path.
I just came back home from a fabulous concert by Midori (more about her tomorrow) and I have to listen to my neighbor practicing rap by screaming "F- that s-!" over and over again.
Somebody please, please, PLEASE poke him in the eye.
The Annotated New York Times. An aggregator for blog posts about articles in The New York Times. I think it would be cooler if there was a similar thing for scientific journals, but I'm not sure if there are enough science bloggers for such a thing to reach critical mass.
A Novel Heroine. About Harriet Klausner, Amazon.com's most prolific reviewer. She reads 4 or 5 books a day--so if you multiply 4 x 365, that's 1,460 books a year--which is both amazing and insane.
Music improves sleep quality in older adults. Note that soft, slow music improves sleep--not rap. Unfortunately, my neighbors probably don't read articles like this. Must be why my quality of sleep has been so crappy lately.
Bloggers Pitch Fits Over Glitches. (via Keats' telescope) I've noticed that Blogger has been wonky for the past couple of weeks. I haven't been really annoyed, though. You can't complain too much for something that's free and I've found that temporarily switching to another browser to post often solves the problem.
Conversational Heavy-Lifting. A lot of people (well okay, everybody) would call me a major introvert so obviously, my conversation isn't what one would call scintillating. Occasionally I wonder what people think I'm thinking about--do they think that nothing is there since I don't run my mouth? Some people don't have anything there even if they do run their mouths.
Will the Internet kill the printed book? "The advent of the Internet has overwhelmed millions of individuals – so much that the relevance of books and libraries are being questioned in this Information Age."
Interview With China Miéville. "I just can’t get with this idea that literature is a twelve-step program. If someone wants to read a book to feel better, and the way they want to feel better is to see that the good people get rewarded and the bad people get punished, that’s fine, but essentially what they want then is a fairy tale." I have some of his books in my reading queue. Not sure when I'll get to them--which means I better get crackin' on all those other books.
Hey, it's another edition of Tangled Bank, this week hosted over at Respectful Insolence. Go and read some excellent science articles. And be prepared to laugh you pants off at Orac's version of Dear Journal Editor, It's Me Again.
Birnaviruses may not be directly important to humans, but it does affect the food supply. The pathogen has been observed to infect fish and poultry among a variety of other animals. Infectious pancreatic necrosis (IPN), for instance, strike salmonids like trout causing the fish to turn dark and bloated and making their guts hemorrhage. In chickens, birnaviruses cause infectious bursal disease (IBDV), an immune deficiency disease in which the B cells are destroyed.
At any rate, this animal pathogen is of interest because Coulibaly et al. in a recent issue of Cell crystallized the virus structure and found similarities between birnaviruses and double-stranded RNA (dsRNA) viruses belonging to a group of nonenveloped icosahedral RNA viruses--that is, the genetic material, RNA, is surrounded by a capsid shaped like an icosahedron but unlike other viruses does not have an additional layer of glycoprotein. This group is further divided into viruses that have positive-strand RNA (+sRNA) or dsRNA. The +sRNA viruses has a capsid with a special fold described as a "jelly roll." The nonenveloped icosahedral dsRNA virus does not have the special fold. dsRNA viruses in the Reoviridae family have a second icosahedral shell which is distinguished by projections that look like "towers."
So what does the capsid of the birnavirus look like? First, the researchers crystallized VP2 from IBDV, the virus protein that makes up the capsid. The protein has three domains labeled base (B), shell (S), and projection (P). Notice that the S and P domains have a jelly roll structure.
The three subunits then connect together to make a trimer.
Twenty trimers make up the subviral particle.
260 trimers make up the virion.
What do all of these pretty pictures tell us? For one thing, the birnavirus protein which makes up the capsid is homologous to both +sRNA and dsRNA viruses. The birnavirus capsid showed projections or "towers" and formed a lattice that looked like the structures of reoviruses. But exactly how are birnaviruses related to the +sRNA and dsRNA viruses? Although the capsid is like those of dsRNA viruses and birnaviruses themselves have dsRNA, the genomic organization and replication strategy of birnaviruses resemble those of +sRNA viruses.
The authors propose one possibility to explain how these viruses are related. Birnaviruses may have evolved from simpler +sRNA viruses. More complex viruses such as the Reoviridae family may have come from a different dsRNA virus which somehow acquired the genomic region coding for the capsid from the birnavirus ancestor through horizontal gene transfer. The resulting virus then expressed more than one capsid protein layer.
One would naively think that the only way to discern any sort of evolutionary relationships in viruses would be through genomic analysis. After all it would be easier to deduce changes through sequence gazing rather than squinting through a microscope. The Cell paper is of interest because it shows that some information about virus evolution can be gleaned from structure as well as genetic material.
Figures from Coulibaly F, Chevalier C, Gutsche I, Pous J, Navaza J, Bressanelli S, Delmas B, Rey FA. "The Birnavirus Crystal Structure Reveals Structural Relationships among Icosahedral Viruses." Cell. 2005 Mar 25;120(6):761-72.
Close your eyes. Imagine that you are walking in Lisbon, in one of the old, traditional neighborhoods. You go into a café and order a glass of red wine. A woman enters. She is dressed in black. And she begins to sing for you.
She flew in for one performance last night and is flying back to Lisbon. How the college convinced Mariza to do this instead of reserving a spot on her next tour, I don't know, but it was indeed a fantastic musical experience. Mariza is a young woman of model-thin build and close-cropped blonde hair. But performing, she is a black widow-wraith crooning fadista rather than a fashionista. I don't understand a word of Portuguese, but Mariza's interpretation and emotional nuance of the genre fado left no doubt that the music had soul.
What was surprising to me was that Mariza is quite warm and humorous onstage and in an informal Q & A didn't seem disturbed at all with the rowdy audience members (diehard fans who drove four hours in the rain just to see her). I don't remember all the questions and answers but here's some interesting tidbits:
- Mariza had a trio of guitarists who played backup--Portuguese guitar, classical (acoustic) guitar, and bass guitar. She has known the classical guitarist since she was five (and he fifteen) and practiced Pink Floyd songs together.
- Fado is a musical genre where ballads/poetry are combined with music. Mariza "writes" a song by doing a lot of reading. When she finds a poem to her liking, she asks a composer (usually a friend) to write music around the poem.
- Fado, and world music in general, is far more well received in Europe than the United States.*
- The Portuguese are very conservative and purist when it comes to fado. Even though Mariza seems very enthusiastic about combining fado styles with other types of music, she believes that the Portuguese would hate any type of mixing.
- Mariza is working on a new album called Transparente (Transparent) where she combines fado with Brazilian rhythms.
*Duh. American over-produced music (where profit has annihilated quality) has obliterated any musical taste the masses had in the first place.
Every time I've fiddled with the radio, there's always this one station that keeps on playing John Mayer's Daughters or Martina McBride's In My Daughter's Eyes. For some reason, those two songs just piss me off. I'm actually rather indifferent to the singers, and the melodies aren't really annoying--not like rap anyway. But I couldn't put my finger on what was wrong until I realized what the lyrics were.
From Daughters: "Girls become lovers who turn into mothers."
From In My Daughter's Eyes: "And though she'll grow and someday leave; Maybe raise a family."
I am no radical feminist, but I resent how songs are so sneaky as to imply that all women are good for are breeding machines--even if the songwriters are saying it in a more genteel way. Well, take it easy, you might say, they're only songs. Oh yeah? Then why is the radio station continually playing those songs? Maybe they're trying to make them into earworms and pound the message into your subconscious.
MUB: Prodigium umbra. Have you ever had any encounters with the monster under the bed? Cryptozoologists fixate on the Loch Ness monster and Big Foot but completely ignore this little beastie famous for terrorizing young children.
I was looking over at the Friday 5ive and one question caught my attention: "Have you ever been a member of a wedding party?" Easy answer: no. The whole ritual in which people throw away money to show they're ready for a commitment that really requires nothing more than a bit of paper is somewhat baffling to me.
And it comes on a stick. Does my neighborhood have "walkability"? Can a kid walk to the store to buy a popsicle without getting run over? Probably not. I've heard of a couple people getting killed on a crosswalk in front of the post office.
The Feynman-Tufte Principle. (via Kottke) Yeah, data figures really should be clear and precise. Unfortunately, some scientists have the habit of cramming as much stuff on one slide as they can--which can lead to one eye-glazing seminar.
Blogs by Women. If you want to sample some women bloggers, there's a pretty long blogroll on this one. (Although I have to say, if you haven't found any female bloggers by now, you're in a sorry, sorry state.)
Doll Parts. (via 2blowhards) For those of you still not convinced that all guys are pervs.
MicroRNA is a Big Topic in Bio. A Wired article about miRNA: "the biological equivalent of dark matter, all around us but almost escaping detection."
Legends are tricky things. Some of them have so many versions that one wonders if one of them was really passed down through the years or someone just made it up on the spot. The Chinese legend about the discovery of the silkworm is one such story. Was it discovered by an ancient empress named Lei Zu as she took an afternoon walk? Was it the Huang Di when he observed a silkworm cocoon dropping into his tea? Or was it Xi Lingshi, a Chinese princess who lived five thousand years ago? Nonetheless the silkworm Bombyx mori has been the center of sericulture for a very long time.
