schmatz's Journal
[Most Recent Entries]
[Calendar View]
[Friends]
Below are the 20 most recent journal entries recorded in
schmatz's LiveJournal:
[ << Previous 20 ]
| Saturday, August 23rd, 2008 | | 5:40 pm |
Nocino
I found a walnut tree back in early July. It's on my walking route between home and the lab. I'm not all that familiar with walnuts, but they're pretty close to pecans so I'm surprised it took me this long to recognize it. There was a big storm that knocked a bunch of young walnut fruits out of the tree so I took about 9 back to my place thinking that I'd bust 'em up and eat 'em. Turns out young walnuts don't have hard shells, they're messy, and they stink. So I had all these nuts and didn't know what the hell to do with them. The internet said that Greeks make a sweet walnut jelly, and the Italians make walnut liqueur. Guess which I chose. So nocino is a liqueur made with young walnuts, sugar, and various spices. It's almost opaque brown and currently smells pretty hideous. It should be delicious in about 9 to 12 months. You use the whole walnut fruit so it definitely requires access to young walnuts, and that's probably why you don't hear much about it. I'm thinking about calling it ノキノ Schnapps in order to squeeze the other axis powers into my walnut drink of evil. So, nocino party at my place around May 2009! | | Wednesday, July 23rd, 2008 | | 10:25 pm |
Shaved Fish
The closest thing to Lovecraftian, noneuclidian horror that I've encountered in daily life is katsuoboshi on my okonomiyaki. | | Saturday, April 19th, 2008 | | 8:55 pm |
Back to the Internet
So it's been about a year since I had an internet connection at home. My monthly internet died for about the 10th time, and I'd gotten fed up with my ISP's tech support. After that I just stopped paying, and the connection stayed down. I submit my taxes online so I recently got reconnected. Now I get to catch up on lj, youtube, facebook, and all that other great internet stuff that I tend to avoid at work. What's been going on this past year? Went on a few trips: Colorado with the family, Sweden for a tRNA conference, and India just for fun. At the tRNA workshop I gave a talk about my bioinformatics/molecular dynamics work with elongation factor Tu (EF-Tu). That work recently got published in the Journal of Molecular Biology in a ridiculously long paper with crazy, full-page figures. EF-Tu, for those of you who don't know (yeah, I guess that's pretty much everyone), is involved in protein synthesis. Every organism has it, and it's been well conserved throughout the past 3.5 billion years or so. It's one of the proteins used to identify the root of the evolutionary tree of life. Anyway, it shuffles tRNAs to the ribosome. tRNAs are adapters that associate a codon (a 3-letter DNA/RNA code) with its corresponding amino acid. These amino acids are strung together to make a protein. It's one of the most abundant proteins in the cell. Oh, and if it breaks, you die. That seems to be a big reason biologists give for studying genes or proteins. If you die without it, it must be important, right? Now give me money for this important research. The India trip was with some of my Biophysics friends. One's from India, and one's from Peru. It was great because we got to go to the Indian's hometown (population 900,000) which isn't a typical tourist spot. People kept staring at me because they'd just never seen white folks before. Seriously. It was pretty fun. At some point a family even asked to have their picture taken with me. We swam in the Bay of Bengal, saw freshwater dolphins in a shallow lake, drove through the backwoods checking out little villages and temples, took an overnight train, rode autorickshaws in the totally insane traffic, ate homemade food, and just chilled in the magnificence of India. People are right when they say that India smells different. It's noticeable as you exit the plane--spicy, dusty, and incensey. Now I'm TAing a class in Computational Chemical Biology, and I just finished my prelim. All that's left of gradschool is the dissertation defense which will probably happen next spring. So things are going pretty well. | | Tuesday, September 26th, 2006 | | 10:45 pm |
Sudoku
You know you live in a bizarre world when you see that many people spend their free moments filling in the multiplication tables to weirdly-constrained, order-9 quasigroups all the while claiming that the task requires "no math". | | Monday, February 20th, 2006 | | 8:13 pm |
Love Song
Whenever I run across the name "Prufrock" I always imagine math rock taken to its logical conclusion (hardy har har). Maybe the songs would give the listener an intuitive grasp of ring theory or Fourier series analysis. Then when you hit that stuff for the first time in class, you're all, "It's trivial! TRIVIAL!!!" But, don't let anyone else in on this idea because you (or worse, I) might be accused of traveling right past the far border of Nerdistan and wrapping back around into the Land of Stoopid. | | Saturday, January 28th, 2006 | | 8:04 pm |
You like me, you really like me!
Remember those papers I submitted awhile back? Well, both got accepted: one to Bioinformatics and one to Computational Biology and Chemistry. So now I'm feeling pretty good about the upcoming prelim. That's the last major hurdle before defending, and it's supposedly much easier when you've got outside verification that your work is science-worthy. Also, it's nice to know finally that I won't have to go back to the material and rehash it for submission somewhere else. Now it's celebration time. | | Tuesday, January 24th, 2006 | | 8:18 pm |
The Long and the Short of It
I'm sitting in on this Biological Physics class. It started last weeek. Today, the prof, who's pretty well known for single molecule fluorescence work, drew a big, logarithmic length scale on the board, which spanned the whole front wall of the classroom. That room is actually pretty uncomfortable but par for the course in Physics departments, I'm afraid. Anyway, he started off the class by asking people to come up to the board and mark where they thought various things belonged. He'd call off "elephant", and the person would mark just past 1 m. The scale spanned from 10^-10 m (Angstrom) to 10 m. People would go until they missed one. We went through wavelength of green light, size of eukaryotic cell, bacterial cell, diameter of DNA, globular protein, lipid bilayer, eukaryotic nucleus, Van der Waals diameter of hydrogen, width of a hair, ribosome, light microscope resolution limit, electron microscope resolution limit, and so on, and so forth. It was a cool exercise. You could tell the biophysics students in the crowd because they knew basically all of them. The physicists didn't know the bio things, and the bio people didn't know length scales at all. So far the class seems set up to make the biophysicists feel good about themselves. It's all old hat, basic review junk. Boundaries between disciplines are wild. It's easy to impress folks because so few people have experience with knowledge outside their narrowly defined field. I think it's a good time to be a generalist or at least someone with the ability to sit back and make connections from biology to chemistry to physics to math to computer science. | | Tuesday, January 17th, 2006 | | 10:22 pm |
The Pirate
58% aliveness, 23% benevolence, 26% intellectualism | You are the Pirate! Yo ho ho, a freebooting life of wild adventure, never a care in the world. Plunder a galleon loaded with treasure, and zip away before the lumbering barges of the navy even know you're there. By evening your stolen booty will have you up to your neck in rum, mutton, and the loveliest lads and lasses.
Yours is a bloody life, yes. But it's such fun. And the clothes! |  | My test tracked 3 variables How you compared to other people your age and gender: | You scored higher than 36% on aliveness | | You scored higher than 0% on benevolence | | You scored higher than 0% on intellectualism |
| | | Saturday, January 7th, 2006 | | 5:55 pm |
Nodnol 871 selim
I'm back from the land of trifle, bread pudding, crackers, silly paper crowns, and bubble and squeak. Visited with the family. Time disappears rapidly around my parents. Days will go by without much of anything happening besides talking and eating. They have this slow, country-style life, and I can dig that. It seems like people are trying to cram way to many damn things into their lives nowadays. Down time chillin' is definitely one of my favorite things to do. No schedule, no plans, no worries. Saw some of the new Doctor Who. It's pretty fun, but I don't really like what they're doing with the daleks and the time lords. There's this crazy thing in British TV where everyone gets to be in all the shows. I swear, there are crossovers all over the damn place. You see Spaced people in Doctor Who, Jeeves and Wooster people in QI, gentlemen from League of Gentlemen popping up in every goddamn thing. I didn't do too much touristy junk during my stay because touristy junk gets old fast, and I've already seen the city a few times. Then there was the unusual cold and tube strike. Saw The Producers in a theatre (<--check the pretentious spelling) near Camden market and browsed through a bit of the British museum which now has this wild, doughnutty, glass dome thing going on in the center courtesy of Norman Foster. Coming back I got bumped up to first class for the trans-Atlantic jump. Sweet. I did that from Cincinnati to Zurich once, too, and I'll never tire of the full-horizontal reclining and constant soundtrack: "Would you like some more wine?" (correct answer "always"). Still, travel karma caught up with me causing 6 hours of delay in my already delay-ey schedule and forced me to spend the night in Chicago due to a cancelled flight. Now I'm back, watching my recently acquired Muppet Show DVDs (thanks, ![[info]](http://l-stat.livejournal.com/img/userinfo.gif) figmynt) and gearing back up for some RNA MD once my phat NCSA account gets reactivated. | | Tuesday, December 13th, 2005 | | 9:58 pm |
Imperial Stouts
It's stout season again, and the local liquor store just got in Bell's Expedition Stout. Bell's is one of many fine midwestern breweries. About half of their line is stouts. There's this crazy Java Stout that has noticeable amounts of caffeine. You get multiply buzzed by that craziness. When talking about stouts, I always have to mention North Coast's Old Rasputin. If you haven't had any, do. If you can't handle it, just pass that shit on the left-hand side. Hopefully I'll be sitting there. There's some other great breweries around here. Three Floyds and New Holland come to mind. Luckily, we have some bars in town that serve these local brews on tap. I know not many of you head out this way, but if you do, I'll buy you a couple of pints (people just don't do the liter thing here) that you won't soon forget. | | Wednesday, December 7th, 2005 | | 12:43 am |
G-town Moves into the New Millenium
A bunch of folks from my hometown in East Texas just popped up on MySpace in the last couple of months. For the past several years, I've been just about the only google-stalkable person from my highschool. A couple have been around on friendster or involved with webby junk, but they're not too easy to find. So the internet has finally made it into the backwoods. Here's to a new era of fruitful internet stalking! | | Sunday, November 20th, 2005 | | 11:28 pm |
Papers Out
Finally, there's been some submitting of papers to journals. Two, both with me as first author. I didn't really write the first one, but it was mostly my programming going into it. We'll see how these go. Acceptance would be great. Rejection has its upsides, too. I could start my career being this wild rebel scientist, shunned by the old guard, spurned for my heretical ideas! Yes, the perfect image of the romantic mad scientist. Or they could publish. Not quite as painful and character-building, but looks good on the CV. | | Saturday, October 29th, 2005 | | 12:33 pm |
| | Tuesday, August 23rd, 2005 | | 8:19 pm |
No Hessian, No Kidding!
Finally done coding up the number-crunching side of this coordinate transform for a Hessian matrix! It's been off and on for a few weeks, now. Sloooooow headway. I'm supposed to be replicating the numbers that come out of Gaussian. I won't go into too much detail because I don't want to get banned. So you tend to represent atomic structures as lists of 3D cartesian coordinates. Sometimes you need a different coordinate system based on bond lengths, angles between two bonds, torsions of two bonds around a third, connecting bond. These are referred to as internal coordinates. When you're concerned with the forces, this is what you want. With cartesians, you can get force constants corresponding to particular atoms, but it makes a lot more sense to focus on the force that a particular bond experiences. Internals also remove problems with whole-system rotation and translation. The Hessian is this matrix of force constants, and I needed to move it from cartesians to internals. Normally, this is done by Gaussian, but Gaussian is typically run in batch mode on clusters so people don't tend to have it sitting around on their laptops. Setting up a run is annoying when all you want to do is jack around with different internal coordinates to test them out. So we're moving that over into a quantum parametrization tool that's in development. Crazy stuff. Next is creating a TCL extension of this. Not my kind of thing. I need my own private code-monkey to work on extensions and GUI junk. Oh, and doing all the sysadmin crap like dicking around with makefiles and making sure libraries are sitting where they should be. Leave all the algorithmic, abstract junk to me! | | Monday, July 4th, 2005 | | 2:03 am |
Japanification
Awhile back, I took a trip to Japan with some crazy San Francisco, former Hausvolk: stellarbaby, confuseme, Greg, and Rachel. stellarbaby posted some of her pics here. This was my first trip across the Pacific and hopefully not the last. Traveling is so ridiculously educational. Worldly is an extremely apt descrpition of the kind of perspective travellers get on life. You see all the billions of little, but essential, details that can differ from place to place. How people talk, how they eat, how cities are organized, what transportation is used, how doors and windows open, what flora and fauna inhabit a place. It's all fascinating. I've run into a fair number of people who dislike traveling because they see different styles as wrong. The windows tilt in from a hinge at the bottom instead of sliding up? The doors slide to the side instead of being push-and-pullable? Water isn't free with meals? You don't leave tips for waiters? People bike, walk, ride trains instead of driving themselves everywhere? Bars and clubs stay open all night long? Beer is sold in vending machines on the street? Nudity isn't outlawed? How on Earth can civilization exist in such perverse circumstances?!?!? Obviously, these foreigners are deeply disturbed! | | Sunday, May 22nd, 2005 | | 7:36 pm |
Callin' the Nobels
In my short experience with the world of academic science, I've seen some pretty amazing talks. A few of these people are doing such impressive work that I believe they'll be up for Nobels in the future. Here's the list:
- Robert Langer - For wack-ass new biomaterials with medical applications.
- Peter Schultz - For putting the smack down on organic chemistry through combinatorial methods. Also for doing work that is the closest thing I've ever seen to mad science.
- Keith Moffat - For the new awesomeness that is time-resolved x-ray crystallography.
| | Saturday, April 23rd, 2005 | | 6:19 pm |
Ten Things Meme
Yes, yes, it's posting time for an old meme. So, a few of these things have probably been done by some of you. Freaks! That's okay, though, I'm not too big on sticking to the rules. 10 Things You (probably) Haven't Done: 1) Been bumped up from coach to first class for a trans-Atlantic flight. 2) Gone headfirst over a bicycle's handlebars into a lamp post. Oh, and landed in a raspberry patch. 3) Pulled a dart out of the back of someone's head after putting it there in the first place (sorry, figmynt). 4) Drank beer (Spaten, no less) on tap at the company cafeteria. 5) Worn a dress and a beard at the same time for no particular reason at all. 6) Been bitten repeatedly by an alligator snapping turtle. 7) Read higher math textbooks (abstract algebra, real analysis) just for the hell of it. 8) Started a kiddie pool skinny-dipping tradition. Some of you know what I'm talkin' about. 9) Kept an inch-long piece of wood within my body for more than half my lifetime. It's still there! 10) Built a multiroom bamboo fort. Bonus: Ridden a unicycle through a cemetary. | | Wednesday, February 16th, 2005 | | 2:10 pm |
Blueberry Morning
Sometimes I buy this cereal called Blueberry Morning, and every time I eat it I think: Oh, what a blueberry mornin', Oh, what a blueberry day. I got a blueberry feelin' Ev'rything's goin' my way. I wonder how common that is. | | Monday, February 7th, 2005 | | 12:09 am |
Coasting
Things have been going really well recently. Freakishly well. My old advisor from the UT RNA lab contacted me about being an author on a paper. I'd done this work on multiple sequence alignment comparison, but grad school started, and it all faded into the background. This will be a chance to salvage that work and get a publication. So that's good news. The bioinformatics class I'm taking is interesting and not too taxing. After this, I'll be caught up on the sequence side of things. Hidden Markov Models, dynamic programming, phylogenetic analysis, sequence searching. I really need to hit some Claude Shannon and Manfred Eigen papers. Information and evolution and how they relate. Besides that class, I've started putting time into learning quantum chemistry. It's good stuff to know, but I want to tackle it on my own. Classes tend to kill my motivation, and this is knowledge I need. The labwork's been going really well. People are starting to use my structural bioinformatics tool so I'm getting feedback. My tessellation project is getting into this fun, graph implementation stuff. I like jacking around with wild data structures and their associated algorithms. Well, what I like is coming up with new stuff. None of this cookbook crap for me. The folks in the lab are hanging out more and more. It feels like we're getting to know each other, and I think that's important for any good collaboration. Lots of the best work has been done by teams of people that really like each other. Our projects are really beginning to merge. We're moving into the same systems and techniques. It's all going to be structural bioinformatics and molecular dynamics for awhile. Last Thursday most of us went out to see the play Copenhagen. It was about an infamous 1941 meeting between Bohr and Heisenberg. There was lots of talk about quantum mechanics, atomic bombs, power, human suffering, and apocalypse. Fun stuff! So things are really chill. There is practically no stress. Every day seems like a vacation. "What do I want to do today? Ah, head in to the lab!" It's fun. Publications and the degree seem almost inevitable. I'll keep chugging along, and I'll accomplish various things. I'm only a year and a half into this thing, and I have significant work behind me. But more than that, I feel really happy a lot of the time. Ecstatically, rabidly happy! Everything just feels right. This is where I should be, this is what I should be doing. Oh, on the downside, yesterday I had a dream where a badger pulled some guy's jaw out of his face. Actually, that was pretty cool, but it freaked my dream self out at the time. | | Monday, January 17th, 2005 | | 3:57 pm |
Winter Break
Last semester ended well. Grades (I hadn't checked them since last winter) were great. I headed home for about a week to visit my parents. Chilled, talked, read, watched movies. My dad just retired so they're thinking about moving back to North Carolina. It might be a loooong time before I get back to the DFW metroplex, and that's okay with me. I recently had to code up quicksort. It's a classic! I'm pretty sure this was the first time for me, though. Quicksort is one of those things that lots of coders implement over and over again, but not me. Never even had to write it for a class. The only times sort's been necessary, I've been using perl or some other language with built-in sorting functions. Anyway, I thought that was kind of cute, and it sped up my tessellation program by a decent amount. Yesterday I saw The Life Aquatic with some friends. I really enjoy movies that are more random and flowy, where the characters are a bit freakish, and you're just along for the ride. Sort of like hanging out with a bunch of weirdos. So I'm partial to flicks by Wes Anderson, Richard Linklater, Christopher Guest, and Robert Altman. Too often, movie characters are given only one or two main motivations for everything they do. One scene, 3 minutes, sets up the driving force behind their whole personality. It's cheap, but what're you gonna do with only a couple hours to play with? You certainly can't cram in the kind of characters you might find in a 600-page novel. So when characters are just characters, and they're not explained, and they have quirks, and seem real, like people you'd meet at a party or the grocery store, I find it quite enjoyable. More theaters need to serve food and beer. The movie would've gone great with a couple pints of hoppy-as-fuck IPA. |
[ << Previous 20 ]
|
