The Book of Joe

Obama picks up huge endorsement.

Tue, 02 Sep 2008 21:58:45 GMT

What?

Last updated 17 weeks ago...

Tue, 26 Aug 2008 20:46:53 GMT

I'm so bad at this.

Anyway, I'm having a hard time finding a lab job. I've applied to around 20 positions, and I've had 1 interview. Of course, it doesn't help that I don't apply to companies that test on animals. But I gotta take a stand somewhere.

I'm planning on moving down to PDX soon. It's a pretty awesome city -- I definitely like it more than Seattle, even though Seattle is bigger.

Does anyone still read this?

Once more unto the breech, dear friends....

Mon, 28 Apr 2008 05:50:54 GMT

P-chem midterm tomorrow.

Do I really know what the Hartree-Fock self consistent field method is? Not really.

But I think I got a handle on most other stuff. Wish me luck!

Edit: I think I got the hard questions right and the easy questions wrong. Meh, we'll see.

I've noticed....

Sun, 06 Apr 2008 03:01:04 GMT

... that I am motived to post on LJ by completely random experiences. Last time it was due a P-chem exam. This time? I just finished a B- horror movie.

So, The Mist was pretty entertaining. It's like what I imagine a B-horror monster movie would be if it were directed by a misanthropic athiest. The plot was essentially an excuse to bash religious fundamentalists and point out that people turn crazy/stupid when society breaks down (new territory, that!). The monster attacks just broke up the heavy-handed political lecturing.

If I squint my eyes I can see an allegory for our post 9-11 world, but the book this movie was based on was written in the 70's. I probably just have something in my eye.

The last 5 minutes were both refreshingly dark and depressingly cliched, but I didn't expect him to go there, so I was pleasantly surprised.

Heh, just noticed this director also did Shawshank Redemption, one of my favorite movies. I suppose he needed a cynical movie to even out his body of work.

I've been reading a lot of Warren Ellis, lately. His revamping of Stormwatch turned a (really) bad mid 90's action comic into a above-mediocre action comic. Relatively, that's a big improvement. And I like his take on superheroes with The Authority. But, really, Transmetropolitan is his best work. No contest. And not a single superpower in that comic :)

Y'all should get your hands on some Transmet, if you haven't yet. Also, Desolation Jones is a newcomer that's a bit in that same vein. Check it.

I have seen the pale horseman of Death....

Wed, 12 Mar 2008 18:56:29 GMT

... and its name is physical chemistry.

Seriously, though. Most brutal exam. Ever. I'll be lucky to get 2/3rds of the problems correct. And I shudder to think about how low the class average will be.

The sick thing is that it was sort of fun. I'm such an academic masochist. I haven't been challenged by a test like that in a long time.

It's not that we were expected to know esoteric things. No, making an exam like that is the easy way out. Instead, we were expected to extrapolate the answers using the information we knew.

For example: We spend half of first quarter learning about particle in a box. Test question? Derive wavefunction for particle in a different shape (won't tell shape, in case someone hasn't taken exam yet and happens to read this). Good times. (I got that wrong, btw.)

Ghosts

Tue, 11 Mar 2008 06:10:42 GMT

Check out ghosts, I'm just digging into it now. This is exactly what I hoped it would be.

-Joe

By the way: Doesn't this, along with Radiohead's recent venture, prove that the old way of doing music business isn't the only way to go? I heard radiohead made like 6 million dollars, which is way more than they would have seen once all the money was filtered through their record label. Sure, it helps that they have about 10^20 fans, but still.

Who needs the RIAA?

Linear B and Chemistry

Sun, 24 Feb 2008 09:46:19 GMT

Your Score: Linear B

You scored

You are Linear B. Even those who can follow you think you're all Greek to them. Which, after all, is true - Linear B being the first known text for written Greek. To most people, you're incomprehensible. But what do you care? You're tough, hard, long-enduring and have greater nobility than most. Naturally, you don't admit to borrowing extensively from your brother Linear A.

Link: The Which Ancient Language Are You Test written by imipak on OkCupid Free Online Dating, home of the The Dating Persona Test
View My Profile(imipak)

Crystal, do you have any idea how often I copy your meme-tests?

And now, for something completely different:

Any physics/chem majors mind explaining the non-crossing rule to me? You know, the one in molecular orbital theory that says when similar nrg levels get close enough together they "mix" and start to repel each other. Explains why sigma and pi bonding orbitals are switched from H2 through N2 (or is it C2? whatever.) My teacher was no help. I don't blame her, it's esoteric enough that I can't find a solid explanation. Either the websites are too introductory or they assume you already know what it is. All I can figure out is that it occurs w/ coupled harmonic oscillators both in quantum mechanics AND classically. And that it has something to do w/ potential surfaces not crossing. I don't even know what a potential surface is. Bah.

Of course, by "any physics/chem majors" I really mean Chris. I don't think any other chem major read this.

Been away for a while

Thu, 14 Feb 2008 02:03:57 GMT

I've not been giving LJ any attention lately. Been pretty busy.

So I'm in Advanced chem, aka AMR light, and it's pretty fun. Just finished the QM midterm today, and need to study for tomorrow's Inorganic midterm. I'm liking the class - dharshi knows what she's talking about.

I'm doing calc II at night. Right now the disk method is kicking my ass. I don't put as much time into calc as I should.

I'm still tutoring M2O and working at the CC.

I was planning on doing 2 credits in the lab, but I really haven't had time to spare so I dropped those.

W3rd.

Been a while...

Tue, 09 Oct 2007 16:47:32 GMT

I've been busy, so I haven't had a chance to update this page in a while.

I'm taking 8 credits in the phage lab, 4 credits of calculus, tutoring Molecule to Organism, and working in the Computer Center.

All work and no play make jack something something....

WOOT

Thu, 09 Aug 2007 21:00:06 GMT

I am done with biochem, done with albany, and coming home!

I had fun here, but I'm excited to be back. I'll arrive at SeaTac saturday at noonish.

He's gone, now.

Mon, 06 Aug 2007 00:09:50 GMT

My parents took him to his favorite dog park. I like to think it was a fun last day, and a painless death.

Thanks for the condolences.

Not a good week

Tue, 31 Jul 2007 21:29:44 GMT

Last friday I flooded the lab after leaving on a water purifier for 4 hours.

Found out my housing situation I banked on for next year fell through.

Sage (my dog) has some sort of bone cancer, and my parents are going to put him to sleep on Friday.

First 2 things aren't really that big of a deal, but god I'll miss sage. I wish I had known that I wasn't going to see him anymore - I don't think I gave him any more of a farewell than a pat on his head.

Haven't cried like this in years.

Yeah, this is me...

Tue, 17 Jul 2007 15:06:07 GMT

New York, New York!!

Tue, 10 Jul 2007 18:12:49 GMT

That's my destination this weekend. Should be sweeeeeeeet.

I got a new cell phone yesterday. It's a huge upgrade from my previous cell phone. And by huge upgrade I mean this is my first one. It's got some pretty awesome abilities, although I get the feeling that they're old hat for grizzled cell phone veterans. Meh, new to me.

Fri, 29 Jun 2007 21:39:36 GMT

I'm going to boston, bitches!

Edit: Boston has singlehandedly affirmed how awesome a good subway system is. Damn you seattle, damn you!!!

Anyway it's big and awesome and I'd totally live there for grad school.

Wed, 27 Jun 2007 20:37:35 GMT

It's like 100 degrees and 90% humidity here. And I thought I'd get a lot of jogging done this summer.

$$

Niagra Falls

Tue, 26 Jun 2007 17:39:16 GMT

Niagra Falls is big. Now, I've known this for some time, on an abstract level. But once you're actually there, and can see the 700,000 gal/sec of water crashing down into the canyon it's carved out, well, the size of the thing becomes a whole lot less abstract. It's pretty damn amazing.

The falls is split up into horsehoe falls (on the canadian side, and accounts for 90% of the volume), Niagra falls, and the relatively tiny Bridal Veil. Bridal Veil may only be about 2% of the total water flowing through all three falls, but it's still fricking big. We went on a tour that took us within about 15 feet of the spot where the water lands; they handed out ponchos and sandles. I rolled up my jeans, took off my socks, and put on some sandals. Getting that close to the falls is insane. Imagine the wettest thunderstorm you've ever walked through, multiply it by 2, and turn it sideways. That's Bridal Veil. They have a no-smoking sign right next to the falls, which is hilarious. There's no possible way to keep a cigarrette lit around there.

I took plenty of pictures. I can't upload them until I get home (Stupid me, I didn't think about bringing a card reader), but my friend Sara has pictures of the trip up on facebook.

Context?

Tue, 19 Jun 2007 18:32:27 GMT

Yes, I suppose my blog has degenerated into science and only science. Now, I'm not saying that's a bad thing in and of itself. But I should pander to my audience, yes I should!

Albany is rather unimpressive. It has some neat big buildings, but nothing to DO. That's why I'm aiming to go traveling almost every weekend. I'm trying to work out taking an Amtrak train to Niagra Falls this weekend and staying for a night in a hostel there. That should be fun.

Me and the other internship kids living in my dorm are also planning on going to Boston for a weekend, and NY City for a weekend. Adirondacks are a possibility as well. That'd be fun.

Last weekend we went to a place called Thatcher state park. None of us brought hiking boots, but we found a great trail (not a lot of work/hiking, but good views). We went underneat 2 waterfalls. I'll post pictures onto my facebook later. It was pretty sweet.

I think I'm going to get a laptop and a wii when I get home. I am addicted to electronics.

Busy days ahead...

Mon, 18 Jun 2007 18:54:07 GMT

Tomorrow I'm going to juggle 3 separate experiments/procedures at once; it'll be pretty hectic. Not as bad as those single step infection curves, but busier than any other day I've had here.

I've been doing the math.. I need to purify , refold, and confirm dimerization/lack of dimerization for 2 proteins a week if I want to finish with them all by the end of the summer. My PI didn't expect I'd finish, but I'd like to go above and beyond. It'll be tough, considering I've only even generated 2 mutants so far. 9 to go, and THEN the purification/refolding/confirmation steps. C'est la vie.

I'm such a tool for stress.

Who woulda thunk it?

Fri, 15 Jun 2007 14:48:29 GMT

Apparently, during a coffee break, my PI was bragging about how he has a great reu student, his best ever.

Which is odd, because I feel really uncomfortable and self-concious in the lab. A lot of this stuff is new to me, and I'm not quite sure if I'm doing it right. But hey, I'm flattered. I guess I can't be doing too much wrong.

A sad day...

Wed, 13 Jun 2007 13:32:28 GMT

Mr. Wizard died today =(

Mon, 11 Jun 2007 14:53:36 GMT

Albany is pretty big (1 million if you include suburbs?), and it has some impressively large buildings, but there's not that much to do around here. On the positive side, I'm getting a bunch of reading done. Time to finish those old fantasy/scifi series I've been ignoring for years. Oh, and I'm exercising too.

The research is pretty interesting. I won't bore you with the details (unless you ask). In a nutshell, I'm trying to figure out which residue of this protein interacts with zinc during dimerization (a dimerization critical to causing toxic shock syndrome). So I'm doing a bunch of site-directed mutagenesis on these 2 separate chains of the protein to change the probable spots of zinc interaction, and then I'm trying to coax the mutant chain to refold with the wild-type partner (don't ask me how that works, no one knows. You just make it very cold and wait a few days, and the proteins are covalently bonded with each other and correctly folded). Then I'm supposed to do some chromatography and see if dimerization occurs in the presence of zinc. If it doesn't, I found my critical residue.

So far, it's boiled down to a bunch of PCRs, minipreps, double digests, and gels.

Good times.

Open Invite

Mon, 23 Apr 2007 19:14:42 GMT

I'm leaving for Albany Once June begins, so if anyone wants to hang out one last time before I leave, drop me a message. We'll make some time!

Georgia Hates Me

Thu, 12 Apr 2007 17:08:05 GMT

U of, that is. Meh.

Current tally: 2 acceptances, many rejections, a few unknowns.

Structure and function studies of proteins related to bacterial or viral infection and host response

Wed, 04 Apr 2007 19:05:36 GMT

Here's the blurb for the lab I was placed in:

Dr. Hongmin Li

My group uses X-ray crystallography to determine the atomic structures of biological macromolecules. Current projects include structural and functional studies on bacterial and viral superantigens, signaling proteins involved in apoptosis, and rational drug design against key viral enzymes. Bacterial and viral superantigens are functionally-related proteins that have the ability to stimulate the activation of large number of T cells bearing particular TCR Vß domains (Li et al (1999) Ann. Rev. Immunol. 17, 435-466; Zhao et al. (2004) Structure 12, 277-88; Wang et al. (2006), Nat. Struct. Mol. Biol., accepted). They have been implicated in many human diseases. The second project is to study the structural and function of a protein kinase and its interaction with signaling proteins involved in apoptosis. The third project is to investigate the structural and functional properties of essential enzymes encoded by West Nile virus, an emerging infectious pathogen. These enzymes include methyltransferase and polymerase (Ray et al. (2006), J. Virol., 80, 8362-70). The REU student will work on one of the projects. He/She will gain hands-on experience of PCR, molecular cloning, bacterial transformation, protein expression and purification. He/She may also learn how to grow protein crystals and possibly how to collect X-ray diffraction data.

Most of that stuff is old hat, but hopefully that means I'll have more time to do things that are new to me, aka x-ray crystallography.

Your Career as a Deadly Assassin (LJ) by maxgallagher
Username
Gender
You first killed at age	5
Your victim was	A deadly assassin
Reason	Accidental
Your trademark weapon	Poison Gas
Your reputation	Deranged and unpredictable
You work with	windn4ch0
You kill for	No reason at all
In the end, you are defeated by	prophet723
Your death	Bullet to the head
Your career body-count	819