Like he likes his food: fast

Posted By on October 6, 2010

.: I’m standing in line behind a college student and a middle-aged man with greasy, short hair. The greaser seems indecisive about his order and instructs the student in front of me to go in front of him. The student quietly declines the offer, and the greaser becomes indignant. Now it’s less an offer and more a command:

“Just get in front of me, what the fuck.”

.: There is no question mark because it is not a question. The student obliges and the elderly lady behind the counter takes his order. I gesture to ask if I should follow suit, but Greaser ignores me. He’s not even looking at the menu.

“Next in line please!” another elderly lady screeches, and Greaser signals for me to proceed. As I place my order*, I see Greaser finally approach the other end of the counter to order from the only attractive and young cashier. He chats her up with nauseating inanities and she smiles all the while.

*Today is no exception:

“Number one with no mayonnaise and a large–”

“Will that be for here or to go?”

“–unsweetened iced tea. For here, and an unsweetened iced–”

“No mayonnaise?”

“No, and an unsweetened–”

“What size?”

“Medium.”

“And what would you like to drink?”

The parking lot seems full oh wait

Posted By on October 5, 2010

I'd never thought I'd curse the fire department so much before I moved here.

God dammit.

They found him anyway and arrested him

Posted By on October 3, 2010

.: My brother thinks anyone can be a journalist, including seventh graders. He sent me this story, via Fark, as evidence:

Hit-and-Run Driver Hides in Tree

Police say the driver of a hit and run crash climbed up in a tree to hide, but they found him anyway and arrested him.

It happened on Hwy 190 and Plano Street in Porterville Thursday night.

Police say Jorge Zavala crashed his pickup into a car while turning onto Plano Street.

After the crash, he ran from the scene but officers found him up in the tree and arrested him on DUI and hit and run charges.

The person in the car was treated at a hospital and released.

.: My brother left a comment, as sure to be deleted as this report, so I will repost it here for posterity:

He drove a hit and run crash?

That just sounds deadly!

Thank goodness they found him and caught him anyway and arrested him.

I just shut my ears when they talk biology

Posted By on September 30, 2010

Note: this entire post, though completely factual, is a setup for a terribly geeky joke. You have been warned.

.: I’m sequencing the maize genome this week. Not the big one in the nucleus, mind you, but the smaller one in the chloroplast. The big genome is about 2.3 billion nucleotides long and would take a dedicated lab of experienced researchers to deduce, whereas the small one is only about 0.00014 billion and can be easily determined by a clumsy grad student.

“Cody,” you ask, “why are you wasting your time sequencing the maize chloroplast genome when Maier, Neckermann, Igloi, and Kössel did exactly that 15 years ago?” Because my maize is different, that’s why. At least, I hope so — that’s what the sequencing will find out for me. My maize is almost guaranteed to have some differences between the published sequence, and it’s these differences I will be taking advantage of.

.: I’ll be sequencing the little genome the old fashion way, which involves the construction of several primers. Amplifying DNA requires primer pairs: each segment needs one forward and one reverse primer (some labs use up and down, but not ours). Amplifying 140,000 nucleotides worth of DNA in ~5,000 nucleotide fragments with overlapping ends requires about 30 pairs of primers.

.: I spent Monday designing my primers. They have to be fairly similar to one another in certain characteristics (melting temperature, GC content, no secondary structures, etc.) while all being unique in sequence. To keep track of them all, simple names are given. The first pair of primers are simply “1 Forward” and “1 Reverse”, and so on down the line. The only reason I mention all this is because designing primers gives me the opportunity to occasionally write down, with perfect legitimacy, “10 Forward”.

The house with a backwards h for a driveway

Posted By on September 26, 2010

.: I had just received my security deposit back in full. I was worried they’d dock a few hundred dollars for scratches on the walls or crumbs under the stove, but they seemed pretty understanding when I explained why I would be moving out. Jersey doesn’t have any branches of my bank, so I mail my checks to my grandfather for him to deposit. As far as I can tell, he doesn’t mind this burden and probably encourages it.

.: My grandfather likes being in the know, so I rung him up and told him to expect a check for $2,000 to arrive soon. “Put it in savings, not checkings,” I instructed him, adultly. “That’s great news, Cody,” he said, adding shortly thereafter, “Listen I’ll just go ahead and tell you: your grandmother and I just had a home invasion.”

.: They were just leaving the house when he accosted them. He told my grandparents to get on the ground. My grandfather didn’t have his hearing aid, so he did not hear him.

“He slapped me around a few times to make me go down faster.”

.: My grandmother injured her foot in the ordeal. He took her jewelry and some other replaceable valuables. The house had an ADT system, but it didn’t help. He wore gloves, a mask, and long sleeves and had clearly done this before.

.: My grandfather finished telling me what happened and mentioned they were driving to my dad’s clinic for treatment. I knew what my dad was going to say, and I knew they would listen to him because he’s a doctor: “Move out of that nasty neighborhood and come live up here next to me.”

.: Thirty years ago, every adult in the neighborhood knew who my grandfather was. He had been the superintendent of the school district, and he was just starting up a new community bank (the same bank I use today, even though the closest branch is in Pennsylvania). Nowadays, thanks to a middle school named after him, the younger generation knows he exists even if they don’t know who he is.

.: They had lived in that house for 39 years, which they had built themselves. Their backyard was a forest, and the neighbors were spaced reasonably apart. Now their backyard is fenced in and bordered by several neighbors, one of which has a shed that my cousin and I shot with a BB gun severals years ago (this episode ranks even today among my stupidest moments, a rather encouraging thought). They’ve resisted all urges to move, long after the rest of the neighborhood started its slow, miserable decline.

.: Christmas is always a difficult time for most families — especially divorced ones — but Christmas Eve was always perfect because my grandparents made sure it was perfect. The lights were the same every year, the tree had the best decorations (miniature baskets filled with miniature chocolates!), and everybody devised new and clever ways to be the quickest to shout, upon first meeting one another that day, “Christmas Eve Gift!

.: As my parents moved from house to house every couple of years, and as I concurrently accrued more and more billable services for which a steady mailbox was required, I started using my grandparents’ home address. Important letters from schools or departments of motor vehicles might have gotten lost or ignored at my dad and mom’s, and moving to a new apartment every year made it a hassle to update every profile and account for every service I used. My grandparents’ home was the only reliably permanent address I had.

.: And now they’ve moved. I found out when iTunes didn’t recognize the ZIP code I had entered for my bank card. My bank account is tied with my grandfather’s, so when he updated his information it updated mine as well. I didn’t know what was going on and it was confusing, but now that I do know what’s going on I don’t feel any less confused. That address is supposed to be there. They’re supposed to be there. It doesn’t make any sense.

.: That burglar stole more than he realized. He stole my grandparents’ security. He stole my childhood. The doorframe my sister and I used to climb when we were small enough to fit. The linen closet I hid in to scare my grandmother. The toaster oven with the worn dials that only my grandmother could make sense of. The deep freezer that always had ice cream in it.

.: Ours isn’t the only family affected, either. As my grandmother got older, housework got more difficult, so she hired a maid. Irma could barely speak English, but she was a hard worker and did the best she could as a single mother to raise her kids. She and my grandmother had the most delightful skirmishes, too. “She doesn’t understand subtlety!” my grandmother would bemoan after returning a small statue of a fairy, once more, to its partially hidden position near the fireplace. And every week Irma would move it back to the center of the ledge — so you could, you know, see it.

.: Now Irma has one less house to clean. And since my grandfather was easily the wealthiest person in the neighborhood, any replacement will be considerably less remunerative. I’m sure he will see to it that she’s taken care of and employed by someone considerate and worthwhile — he’s already guaranteed her children’s college education — but she didn’t deserve to lose this job under these circumstances. But, whatever, right? That man wanted jewelry and he didn’t care how he got it.

.: My grandfather turned 81 in January and my grandmother turned 80 in July. I couldn’t make it to her birthday party, but I did show up a month later to introduce them to my girlfriend. Despite her earlier decree to “stay away from those Jersey girls”, my grandmother found her to be smart and charming. In her turn, she found it endlessly amusing that my grandmother uses words like “hootenanny” regularly and without irony.

.: As we were saying our goodbyes, my girlfriend couldn’t decide if it were appropriate to hug my grandmother or not. I don’t know why she didn’t, but I do know she regretted not doing so. I called my grandmother later to tell her about this confession, and she laughed it off. “You tell her to not be so shy next time.” I realized just now that I still haven’t told my girlfriend that she can relax. I also realized that that was the last time I’ll see my grandmother standing in that doorway.

She Blinded Me With Method

Posted By on March 19, 2010

.: Just a little something I cooked up while the agarose gels:

.: I’d like to put this on a t-shirt, naturally. Any suggestions for reasonably priced custom t-shirt vendors?

Making Stuff Up

Posted By on March 2, 2010

.: Via Jeffrey Shallit I learned of this remarkably fatuous essay in the New English Review called “The Progressive Diminishment of Man”:

The high priests of scientism, from Stephen Hawking to Richard Dawkins, argue that given enough time, science will eventually answer all questions, and implied is the idea that science, and science alone, contains all truth. However, upon examination, we find great areas where science has already abdicated.

.: It’s a cheap trick, but I’m going to employ it anyway. Let us replace all instances of the word “science” with the rather clunky but no less accurate phrase “testing our assumptions, carefully recording observations, and not simply making stuff up”:

The high priests of scientism, from Stephen Hawking to Richard Dawkins, argue that given enough time, testing our assumptions, carefully recording observations, and not simply making stuff up will eventually answer all questions, and implied is the idea that testing our assumptions, carefully recording observations, and not simply making stuff up, and testing our assumptions, carefully recording observations, and not simply making stuff up alone, contains all truth. However, upon examination, we find great areas where testing our assumptions, carefully recording observations, and not simply making stuff up has already abdicated.

.: I do this every time I see someone bemoan the application of science’s methods to a subject they happen to fancy because the subtext seems to always scream, “We used to be able to make stuff up and get away with it, but now those mean old scientists keep asking us for reasons and evidence and unambiguous, coherent definitions to support and justify our positions!”

.: Also, this is just silliness:

Language alone, with its well neigh infinite complexity, were it genetically based, would logically require an immense amount of genetic space. And if language cannot be found in our genes, how could art or culture be found there?

.: We don’t even have to escape the realm of language to reveal how absurd this objection really is. If language is as neigh complex as the author makes it out to be, then how can it possibly be constructed from an alphabet of only twenty six letters? (On second thought, this illustration might not adequately address her objection, if only because I have no idea what the hell she means by “immense amount of genetic space”.)

Among the Fungi

Posted By on January 28, 2010

.: Harvard has a nifty website for the Computational Biology and Functional Genomics Laboratory where one can find valuable tools used in studies of computational biology and functional genomics. One subset of the site is the Gene Index Project, which separates the available gene indices into four broad categories: Animals, Plants, Protist, and Fungi.

.: Not at all representative of the diversity in tree of life, the site has 42 gene indices available under Animals, 47 under Plants, 15 under Protist, and 10 under Fungi. Curiously, under the Fungi tab they advertise the gene index for Phytophthora infestans, more famously known as Potato Late Blight (AKA, the scourge of the Irish). It’s curious because P. infestans is an oomycete, and these tiny guys are as closely related to fungi as fungi are related to animals.

.: It’s a common mistake to group late blight among the fungi, but I would expect the folks at Harvard to know better.

Safety Video

Posted By on January 27, 2010

.: Today my professor had to show the class a tape on pesticide safety, and by tape I mean an actual VHS cassette tape — possibly older than I was. The tracking was terrible, and the narrator sounded like he was speaking through a box fan. When she announced that she didn’t know how to fix it, I jokingly suggested pulling out the cartridge, blowing on it, and putting it back in. So she, without any hint of irony, did.

Dinner

Posted By on January 26, 2010

It's easier than preparing a real meal, in the same way that driving is easier than exercise.