Into each life

The carnival was still there when Kate and I went to downtown San Jose earlier today. We went to the art museum, which had a De-Nature exhibit that was pretty neat. I didn't quite understand the Miro exhibit, but the permanent collections had a few paintings that were awesome -- there's also a photo (or one of a photo from a series) that I remembered seeing in a gallery in downtown San Francisco two years ago. (Which reminds me, if you've never seen Andy Goldsworthy's sculpture / photography collections, check it out. It is Great.)We also went on the ferris wheel that was downtown and noticed that there was another ferris wheel not two blocks from where we were, once we had reached the highest point of the ferris wheel. There was also this mini-ferris-wheel for kids behind us which was cute (it's TINY). Then there was food at the library cafe and the Dr. King Library. I missed it, from the basement up to the weirdly angular and glassy roof, and it was reassuring how little it had changed.

Recap (Thursday now, I believe?):

On Thursday I drove Kate to Valco -- excuse me -- Cupertino Square, where we met Victoria and, after some confusion about the location of "inside of Sears" met up with Kateryna and Lusine as well. I think this was where the person who was selling mops was -- either that or I'm confusing this with Tuesday, but it was kind of boring so I got distracted by the framed prints that was nearby and found duplicates of anatomically correct plant sketches from the natural museum of France and the something botanical society of Britain. Or maybe it was London. (The sketches are pretty.) Whether this happened on Thursday or not, what definitely happened afterwards was Kateryna driving all of us over to Cupertino High School, where school is still ongoing, where we wondered around and visited teachers. We had no idea where Mr. A, Mr. Morse, or Ms. Uji were, but did see Mr. Ferrante, Ms. Mandison, Sr. Murillo, and the French teacher whose name I didn't remember. The high school students were louder than I remembered and unbelievably energetic (did we really act we're high on sugar all the time back then?) but the school itself is pretty much as we remembered it. Except for the fence. Now there's a fence around everything and I think it was either Kate or Lucy who had remarked that now school is more like a prison than ever.

Then we went to Cupertino Square and watched Enchanted, which was ... very Disney. I liked the chipmunk, but the Queen is a bit overdone and the rest of the plot line can be considered amusing, if you turn your brain off (but then, it's Disney). (The tower scene is just...there are no words, but the scene with spontaneous downtown New York parades is hilarious.)

Kateryna, Kate, and Lusine wanted food afterwards, and since Victoria and I didn't, I dropped her back at her place before driving back to Cupertino Square to hang out with the others who were still at Fresh Choice. There were a lot of references that I didn't get and people were amusing themselves with deserts (can you eat jello with a fork? Yes you can -- if you do it fast enough). I drove home afterwards.

There was

The hospital trip yesterday led to a diagnosis of tendonitis, a shot of cortisone, and a prescription for physical therapy for my mom. I learned that mom is even more squeamish than I am when she made the "eww" face and twitched when the doctor brought out a plastic model of the tendon-bond joint in question to demonstrate why she (mom, not the doctor, obviously) was in pain. The doctor said it was partially due to bad design of the human bone structure there and, of course, I immediately started thinking the intelligent design vs. natural selection argument in my head. The engineers may have something to say about putting a tendon between two bones, but the evolution biologists would most certainly point out that considering the joint in question was intended to be used in a life style significantly different from what we're currently putting it through, all things considered, it's doing fairly well.

Phone calls for appointments and things will follow.

Now, for the next recap:

Wednesday was the time-honored Lunatics Movies Day. Kateryna arrived with Lusine. Anna arrived with Malvina. I'm not entirely sure how Victoria arrived but she came also, while I arrived with Soniya. There was food and movies and every one liked Victoria's brown cake. (We had some fun trying to figure out, ahead of time, if there was anything else edible besides chocolate that'd make a cake brown.)

We swapped presents and Anna, despite of being sick, remembered to bring the Hello Kitty coloring book that we got at the arcade in Golfland over the summer. Along with coloring implements. For those who are less familiar with the antics of the Lunatics a coloring book seems harmless enough, if not downright tame and boring. They would then, upon taking a look at the content of the book, be forcefully reminded of the fact that while the Lunatics are many things (loud? Sometimes. Strange? Most definitely) boring is generally not one of them. Ever imagined Hello Kitty with an evil smile? Emo-goth Hello Kitty? Aquamarine bears and Hello Kitty with chicken pox and some sort of Russian remedy that's apparently GREEN plastered on top of each pox?
Like I said: boring is...not so much of a problem.

We watched Ratatouille (Kate hid in her room, courtesy of having watched it a few times too many already). We watched Spongebob (Victoria, Soniya, and I spent different amounts of time occupied with things that are not located near the direction of the TV). Anna threatened us to color the coloring book, or ELSE (everyone laughed, but everyone colored a little too.) I think we watched Meet the Robinsons that day too, though my recollection of the order of movies we watched is a little hazy by now (I watched more movies that week than I did in the six months before). There was a strange pizza for lunch. It was very geometrical with whole basil leaves and perfect transverse cross sections of a tomato fruit laid out on top. It was my first encounter with pizza precision geometry. (Though if Mike knew how to bake pizzas and made pizza for himself when bored he may lay out the topping in some sort of fractal configuration.) (This will only ever occur if no one else is around and is likely to be around for a while, of course.) Anna brought chocolate, which came with a CD of classical music, and we imagined someone sitting alone in a room eating chocolate while listening to...what was it? Mozart? Beethoven?

...actually that would be a very depressing scenario -- eating chocolate alone with classical music.

Eventually the party tapered down to four people again and we watched Pushing Daisies until my dad came and picked me up. Photo from the day:

It's practice

Have finished what I can with the thesis at this point. Later this afternoon I'll be going with mother to the hospital for her checkup, since she has decided that she lacks the proper words to describe her joint ache. (The hospital waiting room is SUCH a depressing place. I'm bringing a book, even if there's a chance that the wait won't be that long.)

A new lavender plant has sprung up in a corner of the garden that's almost (but not quite) at the furthest point from where the original lavender plant is. You have to wonder about that. I've been trimming the bush steadily this year so it hasn't had the opportunity to produce seeds. It could be the roots but then, it's all the way across the yard....

Right, recap time!
Let's see... Tuesday:

Kate's place. I think she warned us that there's not much to eat there right off of the bat. I dragged over all my presents and put them under the tree for Movie Day the next day. I also brought along candy canes (fruit flavored, multicolored ones since the peppermint ones are getting boring) which Lusine and I each had one of when we went to Valleyfair in Kateryna's car.

Valleyfair is crowded. By crowded I mean that it's better than the day after Thanksgiving but there are still enough people around to make you think of a school of those tiny tropical fishes milling around a coral reef. Kate needed to buy presents. Lusine's there to...I'm going to say "soak up the atmosphere", since she did miss Black Friday and I'm sure she's missed the feeling of being stuck in an overcrowded mall (aHEM). We went to the Mac store where both Kate and Lucy immediately proved their ...I don't know what to call it... by using the web access available to the computers in the stores to check livejournals and school grades/email. Kate demonstrated the thing that is the new Mac OS to me. It's very pretty and (I think) much better than anything Windows came up with after 2000. However, being the geek that I am, I remained very sceptical (because really, just how flashy do you need a pictorial interface to be?) and was accused of being a nitpick (while wondering when the heck I'll get to try Ubuntu because really, WHEN?). The new ipods are there. The new iphones are there. I'm not sure if they are the type with or without the phones and either way don't much care.

Food court that day was empty enough (a relative term, I assure you) that we had indoor seating. The guy at the place where I got my food didn't quite know how to use the cash register and I felt bad for him because the line was REALLY building up there. Lusine had something from McDonalds, which Kate was empathetically Not Happy about and expounded to at length why she was Not Happy about it (while I was amused to realize that my mind's somehow established that Kate ranting over her food is a "comforting" sight). (Normality was redefined sometime last year, I think, after the Cake That Would Not Bake incident and before I got used to the toaster.) There were discussions about Christmas decorations in a store, which I really didn't follow, and Spiderwicks movie posters everywhere. We only had to use the cell-phone-location once (like echolocation except shinier and ... not) to locate Kate before we left for Kate's once again.

I think we were warned, once again, that Kate Has No Food In House, Yes. Either way we stopped at the plaza by Homestead and went to Blockbusters where we tried to pick out movies. The actual process isn't so much "picking out" as grabbing all potentially fitting movies and shuffling them through a random elimination process. (We kept Ratatouille, which I was really happy about because I really wanted to watch that.) The Blockbuster place also sold Shrek character shaped candy dispensers with little fans on top which is...neither here nor there, but I remembered it, so you get to read about it. Then, because as Kate has said, No Food, we went to Safeway (conveniently in the same plaza) and got food which isn't really food. By which I mean we got a lot of junk food (no pies though, despite of Lucy's assertions about Pushing Daisies). (I talked my parents into watching Pushing Daisies with me. After three episodes my mom and I went out and bought a pie.) We dumped the lot at Kate's place, petted Kate's rabbit, and rediscovered tinsel. Or at least Kateryna and Lusine did. It comes in different colors and is very...um...shiny. And sheds a lot less than the one we have in the kitchen in Davis and so probably made a better feathered boa. We started to swap presents.

I'll end this recap with a photo from the day:

Check marks

I forgot to include the approach and objective in the introduction portion of my thesis. In a scientific paper, this is essentially the same as writing a literature paper without including a thesis in the introduction. You might be able to figure out what's going on by reading the context but really, it's just a whole lot of wondering what on earth was I thinking when I typed the thing up.

That bit of the editing process didn't feel much like fixing an error. It was more like preventing a pyroclastic explosion.

...

I wonder if I should attempt to recap last week. If I were to describe everything in as much detail as I generally do for the gatherings I suspect I'd end up typing here all night (so, so, should NOT have let the entire week's events pile up but then again -- when would I have found the time and mind set to sit down and TYPE?). If I skipped out all the details then the entire thing can be wrapped up in one paragraph. It will be cut and dry like a page tore out of my agenda... and about as interesting (but definitely neater and easier) to read. There is a magic percentage of details to include for these sort of things but since I don't think I'll be able to find it any time soon I'll, for the records, lay down the basic events and go back and flesh it out over the next few days whenever I feel like it.

Hm. Sounds reasonable.

Let's see then: Lusine arrived on Monday I think. Tuesday I went over to Kate's at noon-ish and met Kateryna and Lusine, and then the four of us went to Valleyfair. We also rented the movies on that day and grocery shopped. Wednesday was Movie Day at around eleven. Soniya, Victoria, Anna, Malvina, and Victoria all made it in addition to Lusine, Katerina, and I. It was at Kate's house again (we did go over there a lot this break, didn't we?) and there was chocolate with a music CD and lots of movies and junk food. Thursday Victoria, Lusine, Katerina, Kate, and I visited CHS, went to Cupertino Square (still getting used to the name) to watch Enchanted, then there was Fresh Choice. Friday was our SF day trip with Victoria, Lusine, Kate, and I. Pier 39...we came back early to Kate's and...I drew on napkins. (It makes more sense with explanations. Or maybe not. Oh well.) Saturday Kateryna, Lusine, and I went to Kate's to hang out. We watched the Simpson movie (DVD) and watched Lucy run around in the backyard. Lusine left Sunday morning.

Monday I went to Shoreline Park with my parents and yesterday, Tuesday, was Christmas. That seems to cover the basic gist of things so, next time will be the details.

When the tea is hot

I haven't typed anything here in a while. Compared to when I started blogger or when I was in my first year at college it'd probably seem like I'm slacking off. In fact, I am slacking off on my posts. I don't update with clockwork regularity anymore and sometimes I wonder if I should. It's as if another small piece of structure-ness is gone from my very scheduled and agenda-ed life and I miss it even though I don't, really. I think a little bit more spontaneity will be good for me. (At least, at this stage.)

I have missed my long, drawn-out, and thoughtful (i.e. reflective and boring) post this year on Winter Solstice. This is my make up post. You have been warned. Flee while you can.

No really, I've given some thought about my blog posts (probably more than necessary). On one hand I think, with some perseverance and self-discipline, this is good writing practice. On the other hand, there is, of course, the time issue. It really doesn't have to be that much of an issue. I don't have to type an entire essay every day (though some of my posts will inevitably ramble on and on, take a detour, get lost, consult a map, wander some more, realize that the map is upside-down before eventually finding their way and getting back to the topic). I CAN type only a sentence one some days (though I'd have to make sure that that sentence is grammatically correct in every which way or else I'll NEVER hear the end of it). It's definitely doable. The main question is, why should I bother? Is the incentive to improve my writing (free-style, no less, and therefore not very applicable to my foreseeable future) enough for me to post 365 times, if not more, per year? Increasingly my decisions are based less on what others want and more on what I want. I'm beginning to do a lot more things for my own sake than for others. I think it's normal. I wonder if it means that I've grown more selfish over the years. I meant to write those two sentences in that order. I start a lot of sentences with "I."

Without doubt I should try to improve grammar for my own sake, even if I wish Kate would stop making those really awful pained expressions every time I trip over my conjugations and declensions. (I think my mistakes actually cause her physical pain. I don't know whether to be worried or amused about this and I suspect I never will -- know, I mean.)

I'm not sure yet, but I suspect I may start developing some sort of a schedule again, starting next (school) year.

I think an extra bit of structure will be comforting then, no matter where I end up.

Right now? Right now I've reached the stage where I'm hit by a wave of nausea every time I think about my applications. I KNOW this isn't healthy and I KNOW it's just nerves and I KNOW I can get it under control in a week, if not less. I'm just not sure if I want to become blase (someone please tell me how to do the little accent marks in the "edit html" window of the blog post window) about all this. It feels good, in a way, to want something this much. In order to have this, however, I'd have to accept the negative side -- the stress and disappointments -- too, and I don't want to deal with that, yet. It's childish, but I want to hold on to this jumbled ball of oh-my-god and what-if and I-hope for just a few more days because right now, this tells me (loud and clear)how much all of this matters to me. I can achieve zen (and maybe talk to one of the Zens; somehow I suspect that Lucy's Zen'd be the one with the most optimistic outlook so maybe I'll try contacting him). It's simple. I just have to enter the mind set that This Doesn't Matter. Nothing to it. And so...I think, "a few more days."

Have I changed at all within the past (calendar) year? I have. Is it for the better? I would like to say yes, except I can't in honesty say that because I have no idea. (How do you add up an irrational infinite series that alternate between the positive and the negative? How can you know, in a sequence of random numbers, whether the final sum would be positive or negative?) (And why yes, holiday time is Writing Time, don't you know? Guess which character I'm working on.) I have no idea about a lot of things. It's very unsettling even though I know that everyone's...in the same boat, so to speak, but then that isn't very comforting either and I'm not the sort of person who's easily comforted anyway so somehow, in the overall scheme of things, it all works out: I don't know if I'm becoming a better person, but I know I'm still trying and that I'm not giving up, no matter what, and that's (almost) good enough. I am still thankful for my friends and family, I still accumulate books and plants (despite of my attempts to stop with the plant accumulation, but I enjoy it too much and so didn't try very hard). I despise exams and enzyme kinetics. I still forget to close the trash lid all the way sometimes but at least I remember to wash the dishes very conscientiously. I still over think things but I'm, finally, beginning to figure out how to simplify some things so that the equation doesn't just overwhelm me with the sheer number of variables that I have to keep track of. Mike would be proud of me. Mike grew three more leaves. (There are many Mikes around.) In the overall scheme of things, another year has ended and... well.

That's pretty much it. Just "well."

Cheers.

Feels like vacation

Worked in the garden yesterday and planted some stuff, reseeded some stuff, weeded a lot (per usual), and harvested peas. We will have a lot of peas. If I don't manage to come home regularly for winter quarter we'll probably have a lot of pea seeds too, later into the year.

I think my dad has finally picked up on my fondness for sci-fi since he drafted me into watching Laserhawk yesterday. We made popcorn from the really colorful popcorn kernels that I grew in the backyard (yep the ones that are practically all shades of the rainbow) (it was actually pretty good) and ate that while watching (I ate most of it, parents being not as fond of popcorn). Yes...popcorn and really bad sci-fi. It's a match made in heaven. Pity that dad can't follow along the English dialogue / plot line (or whatever passed for a plot line) that well, so I was too involved explaining the movie to have much time to point out all the holes in the plot and scientific inaccuracies, which would've been really fun.
I think I enjoy myself a little too much on those occasions but really, why else would bad sci-fi movies be worth watching, if we can't make fun of them?

I watched Paprika just now (thanks Lucy!) and that was much more interesting (my mom finds that kind of stuff too freaky and cannot understand my fascination with them) what with the discussion between dreaming, reality, and the idea of self. (Or maybe I'm over-thinking it, but that's okay, I still enjoyed the anime.) After yesterday's encounter with Laserhawk I'm once again reminded of my belief that...well, if it's sci-fi and you can't do a good job with the CGI, you should just do it animation-style because it looks so much cooler. (But that brings up the whole other issue of the connotation associated with animation and the targeted crowds and so on, so huh, guess not.)

Slightly more yard work, then reading, then maybe something else today. We'll see.
Oh yes. And Lunatics get-together this week!

Why hello there

I am at home now and am slowly coming to terms with the fact that, what do you know, another quarter's gone. (Eep.) I've one book that I tried to sell back this quarter but, of course, it's ended up being the one that has a new edition coming out so they're not taking it back. I was left with a very heavy book, feeling very foolish, mostly because if I had wanted to keep a genetics book I would've kept the one from bio sci 101 which covered pretty much the same material as this book but had much better explanations and diagrams. Kate knows it as the book with the "glowy worms" on the cover, while my current book is, I think, known as the one with the "colored spaghetti" so there you go-- there's further proof that the 101 book is superior since glowy worms beat colored spaghetti any day. (FYI, it's Genetics by Hartl & Jones vs. Introduction to Genetic Analysis from 101 by I don't know whom.)

The cats are been housed at the vet hospital over break. They looked at me most piteously when I dropped them off at Elk Grove but at least they didn't cry (I think being in the carrier that long finally wore them out).

I can't remember what else I was going to type but, essentially, I'm home, my parents try to feed me a lot (currently have a bowl of pineapple on my desk with toothpicks), I've books, and seeds, and a draft of the introduction part of my thesis that I probably won't be touching at all until next week but you know what? Right now, I don't care.
(Ha yes. Be proud of me.)

Getting distracted by the shiny

Get Your Own! | More Flash Toys

Spotted it over at Lucy's and of course went "Ooo well-made flash graphics stuff". The results of which you see here.

If this should be thee, Malvolio

I am finally and temporarily caught up on all my emails, though I'm far from being caught up on my to-do list. Oh well. My schedule is beginning to run away from me, as in, for instance, yesterday when I had class, a hour long break to cram, a hour long meeting with my thesis advisor, a three hour long lab final (which took up nearly all of three hours for me), followed by another two hours in the lab, making buffers and autoclaving things. (And someone took my favorite microscope AGAIN -- this never happen during the normal labs!)

The professor's chemical cabinet smells like the university hospital from when I was little. I don't know whether that should reassure me or worry me. Somehow, I think it might be the latter.

I have one more form to turn in and three more finals, and then it'll be the holiday break for me (well...more or less, anyway). Meanwhile, I think I'll go and do the cyberspace's equivalent of MIA again, just for the next week or so.

Seriously?

No, no, really, I am still alive. I still exist. I panic, therefore I am, etc. The past week has been pretty hectic and while this week looks like it may turn out to be slightly less eventful, for some reason the stress-level has not abated at all (is it better to have a break in-between or to just maintain the same stress-level straight into the finals? I really don't know).

I have had one biochem midterm. This time the average score is much higher at an astronomical 50%. The professor reminded us that she doesn't curve and that, really, we shouldn't panic because there's always the final which is 40% of our grade and so, despite of the final being cumulative, we still have a chance to raise our grades, really.

Monday, when we all got our scores back, was not pleasant.

Today is a mishmash of things. For one thing, it turns out that everyone thought everyone else was going to order micropippets and so, of course, no one ordered them and so I called the company because we really need micropippets. Accurate ones that have been calibrated. And of course the company that does the calibration for pippet brand A doesn't sell pippet brand A, but it does sell B, and C, but not A. The original company informed me that no, they don't do distributors in US anymore so if I want to order anything I can be nice and modern and do it online. They even gave me instructions on how to order things online. It was very nice of them, except the phone call took way longer than it should and I exited the building realizing that A) I have left my bike at the rack across from campus because it was raining earlier and I didn't want to brave the on-campus traffic near the silo and B) I am going to be very, very late and C) that I left my lab keys in the lab and had effectively locked myself out.

Anyway, three hour lab today, and then it's to make copies of this new protocol because we have to switch the DNA extraction protocol since the researcher who came up with the original one informed us that the original one didn't really work that well and this other one works better. The copier machines hate me and one jammed four times in a row (you know those huge xerox machines in the libraries? Now I know how to take out the paper trays and side panels -- all of them) while the other one flat out refused to print. The person who is supposed to fix the machines is as confused as I am and so I trudged back to my mentor to explain that I found primary source for the protocol but the ridiculous compilations of circuits and plastic have me beat and, by the way, I left my lab keys in the self-locking lab.

I suppose that I must look fairly distressed by that point, because Dr. Berry just laughed and gave me a piece of candy.

And then I came home and realized that it isn't even Wednesday yet so, oh boy, tomorrow is definitely going to be fun.

Black fading

Before anyone asks no, I have not uploaded the photographs. My USB cord's in Davis and so I probably won't be uploading much of anything before Sunday at the earliest.

As for everything else, well, our reunion went pretty much the way it generally did. Kate and I arrived first this time and we met Anna and Victoria exiting their car just as we were walking over to meet Christine. I noticed that the lamp in the kitchenware department at Macy's reminds me of jellyfishes and Anna and Christine discovered the hilarity of strange Christmas decorations. Including, but not limited to: diseased goats, over-stuffed birds, and beady-eyed Santas. Soniya even stopped by for a while and we commiserated over metabolic pathways specifically and biochem in general. I found out that I'm possibly still the only person who actually likes the labs, which goes to prove that strangeness does not, apparently, decrease with age.

Lunch at the Cheesecake Factory was fun. By that I mean, of course, "fun" only in the sense that a Lunatics get-together can be. For those of you who saw the photos Victoria's uploaded to her facebook account -- this is where the unicorn-squid comes from. It made more sense in context...well, slightly more sense anyway. Especially when the context was about unicorns, concepts, hypothetical concepts, and contexts. (It was actually an appetizer dish with calamari, but that's alright, we were very imaginative and creative. Especially with the celery stalks.)

The crowd, by the way, was as horrible as you would've expected. Santana Row was only slightly better than Valleyfair but it had the decided benefit of having most of its crowd outdoors where free oxygen-carbon-dioxide exchange was allowed to take place. Also, Victoria is still addicted to hoods but, I'm sorry Victoria, I really don't think anyone's really surprised at this point. (She did buy something else that's hooded, and Anna bought a matching something that's also hooded. I will get the photos up, yes.)

Of course we ended up at Borders. We always ended up in Borders. Only this time we dutifully avoided the children's book section and marveled at the conversion of a Stephen King book into a pop-up book in the sale's section instead. Christine mourned the loss of dinosaurs from "back in her day" and the Japanese store had horsetails (the plant) in ornamental pots. Who plants horsetails as ornamental plants? Asked and answered, I guess.

...

With no transition of whatsoever: I have spent two hours in the garden. The peas are running wild and require their support be put in, now. The slugs and snails got to the radish and the sunflowers but we still have almost all of our garlics, onions, beans, and peas. Something also ate most of the germinating lupines, so I had to put in the seeds again but gardening was still very relaxing (also, the irises and the amaryllis came up and I'm absurdly pleased about that). I took pictures (two, exactly) of the marigolds which I will hopefully upload someday, as well.

...

Went to Michael's today (found the one next to Westgate) and the matting (for frames) are hideously expensive. I wonder if I can just buy the material and talk one of the art teachers into letting me use the cutting boards instead, considering that Mr. Sugita from junior high did give me a fairly good idea of how to cut my own matting. Everything also smelled excessively of cinnamon, which was very strange if you consider the sort of things you'd find at Michael's.

The sum is greater than its parts, but the whole is greater still than the sum of its parts.

Of plants and plans

Another week has come and past and I have not, in fact, started writing my actual thesis yet. It is slightly worrying, but then again, I haven't actually been able to do any of the experiments because we still have to order a bunch of stuff and my mentor is still coping with her deadlines and her French visitors this week, so....

I did get another set of primers to act as a control, get trained for the autoclave, and get an appointment to go in next Monday to talk with the PCR people, so the week's not a complete disaster.
(As far as the project went, at least.)

Thanksgiving's next week and we're plotting the Valleyfair event again. It will be insane there of course, as usual, since it'll be the day after Thanksgiving, and I will bring my camera and backup batteries.
Which reminds me that I still need to find a cat sitter for Simba.

Kate went with me this morning when I dropped Simba off to be carted off to adoption fair, and she has picked up these little ditties from this British TV show called "Black Books" which she sang with gusto. Eventually I got them stuck in my head as a result, and it's kind of strange to have things such as "cows in the morning, cows in the morning one, two, three...! Up 'n at 'em, Up 'n at 'em with a piii-iiick" echoing around in your head. Kate is considering making that bit into her cell phone's alarm clock ring tone and...well, at least it fits with people's perception of Davis. Sort of. The cow bit, not the pick bit. (I suppose it could've been worse. She could've done "I live alone in a tree and no body loves me".)

Here, I even managed to find it on youTube.

Other news? Need to work on memorizing lots and lots of molecular structures. Not fun.

Insanity is Important

While wandering around the plant science building today wondering where my mentor and the autoclave lady went I took some time to consider the importance of insanity in science. I don't mean psychology or psychiatry, though obviously they are important and the people there would be out of a job if insanity is Not Important. I meant the symptoms of mental illnesses, applied more generally to every aspect of science, and how it is that we must often behave as if we are suffering from a serious case of neurosis in the name of Practicing Good Science.

For instance:

Paranoia - Clare has instructed my labmates and I that the generally accepted way of going about doing bacterial inoculation is to assume that "everything got contaminated and we're all going to die". The adrenaline spike that would result, when someone gets THAT thought firmly logged in his / her brain, may help with being extra careful with all the cultures and equipment. Or it may not. In any case it is considered Good Practice.

Obsessive Compulsive Disorder - see twitchy lab interns with glazed expressions. There are really requirements for getting every single detail straight, with accuracies going to a thousandth of a gram or half a milliliter or three nucleotides. Also, there is no other way to explain the the accurate labeling of hundreds of samples, all lined up by date which is, again, Good Practice.

Schizophrenia - when before suggesting an experimental, grant, or research proposal, it's Good Practice to always take a few minutes to pretend that you are a professor -- getting in the mind set is very important especially if you haven't done all the research that you should have -- and look over the proposal. Anything that doesn't make it past your Inner Professor isn't worth mentioning. When applicable, pretending that you're the grant committee might also help, though being in the mindset of that many people at once is reserved only for those with a more serious case of schizophrenia.

Depression - any of the cases where the modeling program, culture, or tests failed. Or also when the resulting data makes you wonder whether or not there are mischievous elves hidden in the lab somewhere, ready to prance around and bang on things once the light's are out and everyone's gone home.

And then I had to leave to go to class.

The haunting of superstition

I had my plant anatomy midterm today, both the lab and the lecture one. The lab one is just a little worse because it, unlike the lecture one, is cumulative. And longer. And involves us sitting in front of a microscope for two hours and getting marked off for EVERY SINGLE TIME we write "parenchyma" instead of "parenchyma cells."

Learning can sometimes be mentally painful. Mostly because, I think, of the amount of time we spend afterwards, banging our heads against a wall for that one really stupid mistake that we never would've made if we had five extra seconds. Or maybe this is physical pain that I'm talking about. I always get the two confused.

In any case, I am not superstitious by nature, but sometimes I really do have to wonder. For instance, our lab midterm today covers up to lab 13, someone took my favorite microscope for the exam so I had to put up with this one with weird focus (some of the microscopes have the knobs in different places, some focus differently -- it's a given that everyone has a favorite microscope and it's considered basic courtesy -- usually -- to leave someone their microscope once they've established their preference), my razor chose today of all days to retire, and I cracked a glass cover slip in half while cleaning up.

If I haven't already failed something this year (really, I have to fail ONE test / quiz / whatever per year, starting since high school -- it doesn't matter if I can make my grade up afterwards or not, but I have to FAIL something each year) (and by fail I mean actually not passing) I would've said that this would probably be the lab practical that I'd fail. As it is, I'm reduced to twiddling my thumbs a lot and wondering just... really, what have I gotten myself into this quarter.

I have RNA primers in the lab drawer though. That is cool.

And then the sun left

There are stores being closed downtown. I went around yesterday and was informed that Scrapbook Alley's closed and moved away and there's a "For Lease" sign in front of Bogey's Books. It gave a depressing twist to the day since that book store is probably my favorite second-hand book store, complete with its strange chairs tucked into odd corners inside and a really awesome collection of photography art books.

Just please, don't let them close Newsstand. I've been getting my eclectic cards there since my freshman year and it's just such a neat little place...and this post is getting more depressing as I type.

Well, since I seem to be promoting things right now I'll post support for the WGA.

I've always wondered at what happens when an artist or writer signs a contract -- at which point does the publisher/company/whatever stop representing "you" and start doing whatever they pleased? (But then, I always felt like signing a contract / putting a set price on artwork is a little bit like selling your soul, so I guess there's really no expectation for an unbiased view point from me.)

On an unrelated note, we got a researcher from France yesterday in our lab meeting to answer questions about Frankia /bacterial symbiosis evolution. I found out that Dr. Berry (my mentor) apparently speaks French and I also got first hand experience of what the French accent sounds like (a lot more British than I figured, which is interesting). The plant-symbiont coevolution's intriguing to think about (kind of like endosymbiosis, except not). Clare gave us a demonstration on inoculation (getting the bacteria into the growth medium to start a bacteria culture), autoclaving (pressure & high temperature steam sterilization), and the lab next door will be getting a sequencing machine next week and we are allowed to use it (once or twice, but still)!

There might be a chance to sequence the short fragment that I'm amplifying (!) to see whether or not I've designed the primer correctly. Of course, since it's a one-shot thing, I better wait until I'm at the RNA stage before I try anything.

I also have to do a percoll gradient and we're out on the materials. Dr. Berry was looking into the PUF grant. ("Have you ever heard of 'PUF'?" She asked. "No," I said, "but it reminds me of the fungi..." and I bit my tongue to keep myself from adding "And Hufflepuff.") (Lucy, I think your influence is penetrating my subconsciousness.) The deadline was yesterday at five pm for the grant and we were talking about it at noon and Dr. Berry wondered if I can get the application and proposal written up by five...which, if I had done, probably would be my closest brush with "the extreme procrastination experience", through no fault of my own. But no, the thing involved a minimum and preferred budget proposal and a discussion on how the reduction of the budget will affect the quality of the experiment and I have no idea what's going on with that part so we're passing the November deadline and are thinking about the one in April instead. (Nothing like thinking ahead right after the threat of the doom of procrastination to distress.)

Midterm next Tuesday. Otherwise, nothing else.

[edit 10:18]
Have found a small glow in the dark star in the back of the car trunk. I wonder when it got there? In any case it made me grin like a maniac and it may very well have made my day.

[edit 10:26]
Remember the Second Life "game" I mentioned a while back? I just saw this article. And a LOT of companies are falling in line for a Second Life in-world representative and Mr. Gaiman's having a PRESS CONFERENCE in-world today.
This is somewhere between awesome and creepy.

More metabolism

Or, as I like to title it, "The Day The Biochem Girls Learn That Atkin's Diet Doesn't Work, and Why".

The short version of the answer probably doesn't make much sense, because it is "if Atkin's diet worked, a lot of people wouldn't be suffering from diabetes".

The less condensed version is this: the carbohydrates that we eat, i.e. carbs, get processed in a series of steps called the "glycolysis", giving us pyruvate (a chemical compound). Pyruvate can either enter the Kreb's cycle (another series of metabolic pathways) via pyruvate decarboxylase (an enzyme) into acetyl CoA (CoA is short for Coenzyme A, acetyl is basically acetate, the chemical, when it's attached to something else), or it can processed via pyruvate carboxylase (another enzyme) into oxaloacetate (OAA, another chemical). Fat (or fatty acyls, as I'm forced to remember them as) is what people try to get rid of when they go on a diet, and fat can only be "gotten rid of" by burning, i.e. metabolizing it. Fat can only be processed ("changed") to acetyl CoA, but not OAA.

All of which is all well and very good if not for the fact that fat has a lot of carbon molecules in it and we get rid of most of our carbon molecules in the Kreb's cycle, and in order for Kreb's cycle to be efficient, we need BOTH acetyl CoA AND oxaloacetate.

Therefore, the people who are on the diet are skimping their carbs and so their oxaloacetate eventually runs low and instead of efficient fat burning the body starts making ketone bodies instead. This is the same as what happens in certain type of diabetes -- i.e. the type that is due to the cell's inability to get the carbs inside of itself. Poor, carb-starved cells also make ketone bodies which leak out ...I think some in the urine, some in the saliva, etc.

I am getting an education. Scary, isn't it?

I metabolize, therefore I am

Just before I left home today I turned, while putting on my shoes, and caught the sight of feet outside of the kitchen window.

The feet were enclosed within sneakers. There were a few inches of denim attached, as well.

After thinking about this very carefully for several moments I concluded that today is, in fact, Not A Wednesday, and therefore there must be a logical explanation for this. Shortly after thinking this there came a rain of decaying plant matter right outside of the window and the mystery was solved. Apparently it was "Clean Out the Rain Gutter Day" today. There was a fence of rather nice mulch around our apartment when I left this morning that was gone by the time I came back in the afternoon. I caught myself contemplating the possibility of growing some herbs in the drainage system.

My plant genetics midterm is today, and there was 23 pages of it which the TA was not allowed to handout until the professor had arrived. The professor was late for quite awhile so we all sat there for nearly the first half an hour of class.

The longest essay-type test I've had in my science classes is around eight pages and it is, coincidentally, another plant genetics class (plant development and genetics, I think, as opposed to the methodologies in plant genetics class that I'm currently in), and we had two hours to do that. The experience was not pleasant (ever tried to design an experiment, predict results, explain your results, then defend your methodologies and predictions with a clock ticking overhead?), it was a bit like trying to write an impromptu thesis (oh God. Doom).

And the professor was late. So we all sat there feeling nervous and put-upon and wishing that the TA would just pass the test out so we can get the stupid thing done with and out of the way.

My hand was cramping by the time I left (two minutes before time was up -- we get whatever was left of our two hour class period).
The test was somewhat poorly written too.

On the plus side, Dr. Berry emailed me just now to tell me that the primer has arrived and that I can go and pick it up tomorrow (PCR, here I come).

Somehow it's not cliche

I'm still at Santa Clara, though I should be going toward Davis soon. Meanwhile, while I have a few minutes on hand, I thought I'd share what I saw at the Walkers Design Museum the other day. They're doing a "Peace Starts Here" exhibit (or something along those lines -- I've forgotten the exact name). I was initially skeptical at first -- you don't spent the past however many years in a relatively liberal area without learning a thing or two about grassroot type peace movements and the quality of art that usually results -- but I was very pleased to find out that the thing was...pretty awesome actually.

There is an organization that calls itself the Nuclear Age Peace Foundation that went out and hired a design firm for the project. I've looked it up -- it's called the Chen Design Associates. The exhibit is idealistic to the point that it verges on the edges of being cliche but the visual displays and creativity managed to salvage that and make it look cool. It's quite impressive really.

My favorite is a wall where there are hooks and slips of colored paper cut out that have holes on them, and a marker. There're instructions to leave a "message of peace" on the wall, and as I went in each different time (first time to look, second time to take picture, only to have low battery message displayed on my camera, third time it isn't open, and finally the forth time where I actually got the pictures) the wall has been steadily filling up. I'll post a few pictures here, the rest (along with two of the other displays besides the wall) can be found under the Shutterfly link.







You get a fairly diverse crowd, obviously -- and I don't mean just the different languages that show up, but also the different messages indicating vastly different personality types (i.e. it's not all new-age hippies). There are the messages that say "say I love you more" and then there are the messages that say "do acid", so you get different shades in the spectrum, and it's all very neat.

Why yes, I did leave a message there too.

Higher and deeper

Vague mess of deadlines and treading in other people's disorganized mess - that is what my life has been reduced to, at this point. I have just spent almost half an hour sorting through emails and other deadlines and things and it's mind boggling how fast the dreariness gets to you, even on a Friday morning.

On the other hand, I'm going home this weekend, so that should be interesting.

Halloween has passed rather uneventfully this year. Not that many people dressed up and the next day I heard people telling each other how they only had TWO trick-or-treaters the entire evening. The labs where the TA cracks truly horrible plant-jokes are on Tuesday and Thursday only, so I didn't get to see whether or not anyone dressed up. I did, however, see three guys dressed up as Tetris blocks in their painted, highly cuboidal cardboard costumes dash into the middle of the bioenergetics lecture, run up to the platform, fit their squarish costume pieces together, bounce up and down a few times, and then dash back out. There was a moment of pause right afterwards and then the professor asked, looking very confused, "Does anyone know who they are?"

Angela said she'd managed to take a picture of that. If I can get it from her I'll post it here.

That pretty much concluded my excitement for the day. That and the fact that I (finally!) ordered the primers. So now it's keeping my fingers crossed that they'll work. If not, it's either back to the designing stage or attempt to do something with enzymes, instead of the DNA sequence that codes for the enzymes.
...at least I'll get to learn how to do PCR.

It's Friday. Cheers.

Canis meus id comedit

Today my TA drew Casper (the friendly ghost) waving around a strip of cloth on the blackboard (which is green -- the board, I mean). He explained that Casper was stripping, and so it was the Casparian strip! (The Casparian strip is a layer of wax that is around a specific cell layer in the roots of plants so stuff in the dirt doesn't just randomly get in and out of the plants. Stuff, i.e. solute, movement is regulated, see?)

I didn't know which was louder, the laughing or the groaning. Lucy, you would like him. All things considered, this is the same guy who claimed that strawberry runners are popular in baseball because of all the stolen (stolon)(botanical term for the runners, i.e. modified stems) bases.

Meanwhile, life continues. Simba has discovered that I'm not wearing jeans this week and so he can get me to make funny noises by sinking his claws (they're starting to grow out again since when they were last trimmed) into my legs. Plant anatomy classes offered us pumpkins to take home today and so I took one that has the coloration and shape of a stunted basketball home with me. Kate's decided that it should be placed on the counter, where we can stare at it, and so this has been done. My scholarship application is due tomorrow and I am currently on my third cup of tea. I also have not done the dishes, despite of the fact that I have finished dinner more than five minutes ago. However there is no one around to critique my lack of promptness in terms of dish-washing, so all may be well still. Mike (the avocado, not the fictional character and most certainly not any of my classmates) was planted into a pot on Sunday and seems to be doing quite well out there on the balcony along with our -- excuse me -- MY moldering pots of bromate-heavy dirt. I plan to take the plant home with me at the next available opportunity, before the chemicals in the Davis water can get to it. I think I've grown fond of Mike, despite of the fact that I don't particularly like avocados.

Gosh, Halloween's on a Wednesday this year, isn't it? I should consider going into hiding tomorrow night.

可以这样说

一个学生的生活可以这么解释: 以他丢了的铅笔和一页一页的作业写出一个个等试来描述他在三维空间和四维时间中画出的弧线. 数字和字母支撑着他的天地. 他的家藏在横格本之间的某个地方.

一个朋友的生活可以这么解释: 以他所乐意付出的一切和他的笑容. 以回忆. 以玩笑. 以那些所有摸不到的东西, 和照片一起放进影集, 带在心里. 它们总会在那意想不到的一刻出现在面前.

一个人的生活可以这么解释: 以他的理想和他的需要在家友的支持下盖出他的梦, 建出他独特的一生.

Melange

Brace yourself, it's going to be one of those posts.

There are some resolutions to the pile of deadlines yesterday. The first one I think I'll mention is the problem set, which has caused me no end of headaches with its poorly worded problems and mistakes. It ultimately resulted in me attending the TA's office hour (well, part of it, anyway). I'm proud to say that I've managed to get the TA to clarify (i.e. give hints to the class for) one problem, to fix a rather important typing error (he gave us the wrong genotype, i.e. genetic makeup, of the plant) for another problem, and to cancel yet another, half-page long, problem entirely. Between Clare and I we've managed to get him to clarify a fourth problem and push the deadline for the problem set back one day. My accomplishment of the day(and how sad is this?)probably is walking the poor TA through why the genetic recombination frequencies that he gave us won't work, why they still won't work even if he got rid of the four highest numbers (which he suggested), and ended up with him checking with me for the right answers for the fifth problem. I felt bad for the TA, but he should've looked over the problem set before he handed it out in class.
I finished the rest of the problem set while waiting for my class.

To contrast with that I can mention some of my scholarship application woes, which most revolve around the advising service UCD provides where advisers read and comment on your application essays. The first day I went in the person who is charge was at a meeting, and the people at the front desk didn't know what to do, so they had me drop off my essay with my contact information with them. When I failed to hear anything back, I went in the next day only to find out, after more confusion with different people at the front desk, that the person who is in charge was actually going to be gone for a few days, and I was sent to someone else, who couldn't find the paper that I dropped off, and so she suggested that someone else had probably picked it up and asked for me to check again Friday morning. I have found out recently that a pre-graduate adviser has ended up with my essays and that I can get them back next Tuesday at the earliest, which is exactly one day before the deadline.

I am half way through my reading and have been instructed to abandoned degenerative primers. The plan is to go on with the primers that I have, provided that I don't find anything else too interesting this weekend.

Also, I biked into two bees today. The first one smacked straight into my forehead while I was about three minutes away from campus and buzzed quite angrily in my bangs for a few seconds before I could shake it off. The second one happened less than a minute later when another bee bouncing haphazardly off of the side of my head. It's... just one of those days.

But- (and there always is a 'but') I did learn why fats contain more calories than sugars today in terms of biochemistry. It is because fat molecules (well, mostly fatty acids) are far more reduced than sugars, and so have a lot more electrons. Therefore when you metabolize fat the change in Gibbs free energy (thermodynamics, can be calculated with an equation which I don't remember) is much more negative and more energy is released, so you get more calories out of fat. Compared to fat, sugars are partially oxidized already, and so contain less energy.

Which reminds me: midterm's on Monday. Cheers.

In which the deadlines builds up

I found out that there is a Zach in my plant anatomy class today. He looks nothing like the fictional character, of course (well, he is Caucasian, but that's about it), but mostly I was just pleased to encounter the name in real life.
Speaking of plant anatomy, I had to take a cross section of a pea sprout's root today, as close to the root tip as possible. Since the slide samples usually need to be fairly thin (within 5 cell layers is excellent) and the roots are colorless (white, therefore containing no pigment or chlorophyll), the resulting 1mm diameter slices are very, very hard to see. Both my lab partner and I each lost a slice today. In the end it was faster to try to make another slice than to look for the one that is probably still out there somewhere - its nebulous presence swirling down the drain with the rest of our lost plant tissues, t-blue dye, and DI water.

Need to do: scholarship application, study for midterm, project (breeding program for potatoes with high starch content, I THINK), problem set (less than 10 pages, cheers), thesis background reading (around 20 pages this week), design degenerative primers (first time for everything, right?), and thesis outline, etc.

Kate has just discovered the joy of fat crystal squirrels ("It looks like a chipmunk! She exclaimed, while I stared at her.) It came along with the one of the Christmas gift catalogs and has made her day - not to mention fat-squirrels-induced glee. I told her that I don't understand her and she told me that I haven't looked at it long enough to fully appreciate it and we wondered whether my amusement at how easily she is amused makes me easily amused as well and... yeah. Happy Thursday, everyone.

Nonplants and waffles

I think, having read about Lucy's dreams lately, my subconscious has decided that I need to have more dreams of my own, and so I had a dream and, unfortunately, I was in the plant anatomy lab midterm again. The only thing that made the dream midterm different from the real midterm was that the TA, instead of asking us questions about the slides of plant stuff projected on screen, was holding up plant stuff for us to identify. This is, still, within the respectable boundaries of normality. At least it was until the TA held up a giant fuzzy microbe -- or specifically, a giant fuzzy microbe that looked exactly like the dinoflagellate (i.e. sea sparkle) that Kate's got me for my birthday -- and asked us to identify it.

My first thought wasn't even "wait, there's something weird with this." That was my second thought. My first thought was actually something along the lines of "but that isn't even a plant!" -- which is, yes, very sad. And then I realized that I'm dreaming and so this dream ended and another one began where I spent a lot of time running around between classrooms and being almost late for everything (FYI: if I dream at all right after finals and hard midterms they inevitably end up being stressful and school-related), and eventually I woke up thinking "I really want some waffles."

I didn't really understand it either, since at no point did any memory that can even be remotely related to waffles surface in either dream. I still crave waffles though, and I think I'll probably end up spending the rest of the day thinking about the strangeness of my waffle-inducing (why? I ask you -- WHY?) dreams.

finem

[edit 16:07]
You know what's a really SCARY name? Gamma-glutamylcysteinylglycine.

On nomenclature, or not

Kate and I had a conversation the other day which began with her narration of how she was helping out with the decorations for something and how no one except her knew how to spell "piranha."

I said, very intelligently, something along the lines of "there's an 'h' in there somewhere, right?" which of course led immediately to hand waving and exclamations of "that's exactly what everyone else there said!" so I pointed out that, hey, at least I learned how to spell "cephalaspidomorphi" (zoology class, what fun), and Kate retorted that piranhas bit people. I argued something along the lines of that cephalaspidomorphi evolving earlier which was again turned aside by Kate's statement that piranhas bit people, which, I was led to believe, thoroughly trumps all other characteristics of any organism. I then remarked that with ideas like that, that must be where her rabbit gets her beliefs, which led to a good laugh since her rabbit DOES seem to think along the principles that while being Cute and Fuzzy is well enough, as far as modus operandi goes, Biting People is For The Win.

To be fair though, she hasn't bitten me at all since Kate came back. I think she's bitten Kate, but she always bites Kate, so I'm not sure if that counts.

Meanwhile, I have the bioenergetics midterm left. Today's lab midterm for plant anatomy is astonishingly hard, being that it contained a part where we had powerpoint slides of things we had to identify as well as a part where we were given two pieces of plant and had to prepare and dye the plant samples, make the slides, and then name all the tissue, cell, organelles, and visible cell metabolic products that we could see with a light microscope. (There are very many things.)
Eye twitch, I've concluded, is an inevitable occupation hazard.

人在旅途

明天考试. 目前好像大部分还在按顺序进行.下一关, 我想, 应该是下周一, 为下个学期报课的时后. 今年是否毕业大概也就靠它了.

In which deadlines loom

The UCD registrar has informed me that the schedule of classes for winter quarter will be available next Monday and the registration for classes will begin a week from that date.

That gives me a moment in time where I tried to think in expletives. I didn't get very far, being distracted half way, already, by whether or not it'll be possible to schedule classes around labs or labs around classes.

Speaking of labs, I had my second lab meeting yesterday with my fellow lab members (consisting of three graduate students and three undergraduate students, four counting myself) and we discussed possible projects which mostly didn't include me since I'm sort of on my own project already (I THINK I may have two sets of possible primers now). The subject of the colonization of acidothermus (a bacterial that's the closest relative to the symbiotic bacteria that I'm working on) came up, since acidothermus only lives in hot springs and yet somehow they have colonized hot springs all over the place. One of the grad students suggested that it may have traveled on the feet of birds, which is how we ended up discussing the possibility of ecological studies, traveling to exotic places in South America, and swabbing the feet of flamingos.

I found the idea of swabbing the feet of flamingos amusing. Mike (yes there's yet another one - there are so many Mikes around it's beginning to alarm me), a fellow undergrad, asked whether or not we were serious, at which point all of us, Dr. Berry included, cracked up.

By the way - about the peppers - I'm beginning to think that my social sci friends may need to go and teach my biotech classmates. (How is it you guys know about this and they didn't?) You'd think, judging by their expressions when the professor was explaining about the peppers, that it was back in whatever century it was and Copernicus had just informed them that the orbit of the sun isn't centered around the earth. I was, personally, surprised that no one brandished words like "blasphemy" and "heresy" around. I guess this just goes to prove something that Dr. Rizzo, from my freshman year, had said: there will be people who can tell you the exactly DNA sequence for a certain trait in a plant, but who will have no idea what the actual plant looks like.

For what it's worth, I'm glad I've picked up some of the practical knowledge about plants before I went in depth about the molecular bio part.

[edit 17:40]
If you've typed the word "cells" hundreds of times when you're in a hurry does that excuse you from misspelling the word, even if you're majoring in biology?

Excuse me, I have to go and feel stupid now.

In which I face primers and more cat fur

It is, unfortunately, a Wednesday.

I intensely dislike Wednesdays.

All things considered though, the events today haven't been all that bad. The pacing of things have picked up, certainly, but that has more to do with the progression of the quarter than Wednesday in particular. At this point I'm pretty sure I'm just biased against the day for the principle of things. It would probably be better if I'm living with a bias for a specific date such as Friday the 13th, for example. Those come along far less frequently and would probably lead to a much more productive life than one where I spend every Monday dreading Wednesday.

But then, you know, that's just one more of my many idiosyncrasies.(Did you know that "idioplast" in botany means a cell that looks different from the cells surrounding it? I'm guessing that "idio" is the root.)

As far as lab work went, I got around to designing primers today which, to put it more accurately, wasn't so much me "designing" the primer as me selecting conserved regions of DNA, counting the nucleotides and combinations, and plugging it all into an online program (123 Genomics is your friend). There was some confusion about the sequence because one of the sequenced genomes was the whole genome, so I need to find out which part of it was the code for the enzyme that I needed. The whole process took somewhat longer than expected and I had to literally run off to my bioenergetics class. I missed the few vacation photos that the professor usually would show in the beginning of each lecture but that's okay, Angela told me that we had birds today, and boobies are no where near being my favorite bird (though you have to give them credit for having a name that is based on the word for "crazy person").

I found cat hair on my desk today, which is puzzling since I don't let Simba into my room. It may be one of those mysterious cat things. Or else Simba has learned how to walk through walls which, although it'd be pretty awesome, would also be kind of creepy and possibly highly annoying. Do I really NEED to be poked awake at 4am in the morning? I think not.

FYI: I just realized today in my plant genetics class that people outside of botany / horticulture / agriculture related fields, who don't grow things much, probably don't know that red bell peppers and green bell peppers are the same thing. Yes, you heard correctly, they are actually the same type / cultivar of plant. When the peppers ripen they turn from green to red. The professor said that that's why red bell peppers are more expensive -- because they have to stay out in the field longer and so run a higher risk of being damaged (bugs, diseases, etc., i.e. pathogens). She also said that that's why red bell peppers are generally sweeter which, personally, I've never noticed, but then I don't eat raw peppers that much and she does, so I'm going to take her word on that.

周三的孩子

这学期的事已经开始忙起来了. 有考试,实验乱七八糟的一大堆. GRE考试分数昨天来了. 爸把它扫进电脑,寄来, 所以我报大学应该算是进入第二步了.

Further geekage

Because of course we can never have too much, right?

This's supposed to be a book meme copied from Makani along with the directions/descriptions:

These are the top 106 books most often marked as "unread" by LibraryThing's users (as of today, 30 September 2007). As usual, bold what you have read, italicise what you started but couldn't finish, and strike through what you couldn't stand. Add an asterisk to those you've read more than once. Underline those on your to-read list.

[My to-read list is still over 100 books long, by the way.]

Jonathan Strange & Mr Norrell
Anna Karenina
Crime and Punishment
Catch-22
One Hundred Years of Solitude
Wuthering Heights
The Silmarillion
Life of Pi : a novel
The Name of the Rose
Don Quixote
Moby Dick
Ulysses
Madame Bovary
The Odyssey
Pride and Prejudice
Jane Eyre
A Tale of Two Cities
The Brothers Karamazov
Guns, Germs, and Steel: the Fates of Human Societies
War and Peace
Vanity Fair
The Time Traveler's Wife
The Iliad
Emma
The Blind Assassin
The Kite Runner
Mrs. Dalloway
Great Expectations
American Gods
A Heartbreaking Work of Staggering Genius
Atlas Shrugged
Reading Lolita in Tehran : a memoir in books
Memoirs of a Geisha
Middlesex
Quicksilver
Wicked : the life and times of the wicked witch of the West
The Canterbury Tales
The Historian : a novel
A Portrait of the Artist as a Young Man
Love in the Time of Cholera (Though in my defense it was in Spanish and my Spanish isn't that great.)
Brave New World
The Fountainhead
Foucault's Pendulum
Middlemarch
Frankenstein (The introduction just got way too long.)
The Count of Monte Cristo
Dracula
A Clockwork Orange
Anansi Boys
The Once and Future King
The Grapes of Wrath
1984
Angels & Demons (Will never read willingly. I've enough of the style.)
The Inferno
The Satanic Verses
Sense and Sensibility
The Picture of Dorian Gray
Mansfield Park
One Flew over the Cuckoo's Nest
To the Lighthouse
Tess of the D'Urbervilles
Oliver Twist (Chinese version.)
Gulliver's Travels (Chinese version.)
Les Misérables
The Corrections
The Amazing Adventures of Kavalier and Clay
The Curious Incident of the Dog in the Night-time
Dune
The Prince
The Sound and the Fury
Angela's Ashes : a memoir
The God of Small Things
A People's History of the United States : 1492-present
Cryptonomicon
Neverwhere
A Confederacy of Dunces
A Short History of Nearly Everything
Dubliners
The Unbearable Lightness of Being
Beloved
Slaughterhouse-five
The Scarlet Letter
Eats, Shoots & Leaves
The Mists of Avalon
Oryx and Crake : a novel
Collapse : How Societies Choose to Fail or Succeed
Cloud Atlas
The Confusion
Lolita
Persuasion
Northanger Abbey (Pride and Prejudice remains her best work, I guess.)
The Catcher in the Rye
On the Road
The Hunchback of Notre Dame
Freakonomics : a Rogue Economist Explores the Hidden Side of Everything
Zen and the Art of Motorcycle Maintenance : an Inquiry into Values
The Aeneid
Watership Down
Gravity's Rainbow
The Hobbit
In Cold Blood : A True Account of a Multiple Murder and Its Consequences
White Teeth
Treasure Island
David Copperfield (If only to figure out why Kate keeps making those references.)
The Three Musketeers
Bastard out of Carolina

In retrospect that didn't seem so bad, after all.

Licensed geek talking

The first disease that I can think of which links kidney problems with blindness is diabetes mellitus, but kidney isn't the cause of the problem. I can't think of anything else based on my knowledge of what the kidneys do (waste removal, promote production of red blood cells) (which I always found strange because to me it makes more sense if the liver's in charge of the promoting)(come to think of it, if certain wastes build up in the body that COULD cause blindness, but I'm not sure if this will occur before the other toxins have reached critical levels) so I've looked it up (courtesy of Google Scholar, which is handy) and there's an article (2005) about how there is a disease called Senior-Loken Syndrome where the patient'd get kidney disease (nephronophthisis - don't ask me how to pronounce this, I have no idea) and a form of blindness (retinitis pigmentosa). But then, this has been traced to a defective gene, and so kidney is, once again, not the cause of the disease.
So I'm sorry, Kate, but I honestly don't know.

Also, honestly, I find the fact that I've bookmarked pages like "Molecules to Go" and "123 Genomics" far more worrisome than whether or not my spelling is better when I'm talking - er, writing - science-speak.

While I am taking full advantage of my geek license however (and thank you, Lucy), I'd like to link you guys to something pretty. This, ladies and gents, is what I spend about six hours per week looking at:

Lab 3 photos - from last week. Medicago is alfalfa, and the stem's stained with t-blue, which is toxic. Come to think of it, all our dyes are either corrosive or toxic, but we're required to use neither gloves nor safety glasses. I guess at this point they just assume that we're neat-fingered...with, I suppose, good reason. After all, parts of those six hours require us to do cross sections and longitudinal sections of plant materials that are usually 1 cm long, with razors that can get "dull" just by touching it to a hard surface, such as a table. You either get to be neat-fingered or you get stitches on your fingers (which has happened to a student before, I heard), so that's ...really not much of a choice.

Lab 5 photos - stuff from this week. You HAVE TO scroll down and see the Tillandsia scale. It's the blue and purple thing that looks like a weird tropical sea creature. Tillandsia is the Spanish Moss, and the scales are what make the plant look whitish. The scales help the moss absorb water. The so-called scales are actually a type of trichome. (And Spanish Moss is pretty neat plant-wise too and no, it's not an actual moss. Kate wanted to keep some last time I dragged her to the conservatory, so we took a bit home but alas, our apartment is too cold and dry for the tropical plant.)

Oh God it's Friday.

When multiplication means the same as division

There was some confusion about cell replication today which, all things considered, is kind of sad (i.e. - all things meaning that this is an upper division class and most of us have been going through the cell cycle since before high school). But - fear not - there will always be confusion. For instance, today the TA informed us that after the first part of meiosis (meiosis I) there is, in fact, no cell division (cytokinesis) and, in fact, there's not going to be a cell division until the entire meiosis's done with and both the chromosome number and the chromatid number have been reduced by half.

We stared at him. I'm sure our expressions said, very clearly, that we thought that he had lost his mind.

Most text books depict a cell division after meiosis I. In fact, most text books SAY that there is a cell division after meiosis I. I've checked, having spent considerable time in-between classes today musing over the different images of the cell cycle that I've been forced to remember within the past however many years. There will still be confusion but, if I'm lucky, it will have dissipated somewhat by the time of the midterm.

Yeah, that's always good.

Bioenergetics is as enervating as usual. We learned about creatine today which is, as it turns out, a very important compound in the body and a medical diagnostic tool to boot. Creatine's a rather oddly shaped compound (though no more oddly shaped, I suppose, than any of the other things we've been looking at) that's responsible for maintaining a steady pool of ATP (adenosine tri-phosphate) in the cell. It sort of functions as the molecular equivalent of an energy storage battery type of thing. Medically it's used to test (via blood sample) to see if someone's had a heart attack since cell deaths in the heart will cause a lot of the creatine kinases (enzymes that catalyze the reaction between creatine and ATP) to be released into the blood from the dead cells. So high concentration of the kinase (abbreviated CK, I think, on the blood test) is bad news.

Also, creatine has a constant turnover rate where the body steadily converts it to creatinine, a waste product that's processed by the kidney. Therefore, elevated creatinine level is a prelude to kidney failure.

Now see, all this would be so much more fascinating if I don't have to remember the structure of the organic compound. I had thought that memorizing the structure of the 20 amino acids was bad. Clearly, I thought wrong. It's a measure of how far I've come when I find myself looking back and feeling nostalgic about the days when the most complicated compounds I've got to know are things like sodium bicarbonate and dinitrophenol.

Those were the days.

And that concludes your five minute adventure into the wonderful world of biology. Congratulations.

Some sparks of humor

The other week a few classmates and I were sharing stories about the mishaps we've encountered with the new freshman population on campus. One incident, if I recall correctly, involved someone who came out after class to find that someone else had chained his/her bike to hers. The hypothesis was that the person was trying to loop the bike lock around the pole, but for some reason didn't think to go around the other bike that was already there and instead went THROUGH the other bike, causing much grief when the classmate came out and wanted to leave. With her bike.

There was a story where one of my old dormmate got run off of the side walk by a freshman on a bike. Another one of my classmates said that he'd stand around with a protest sign for that, if he could find the time for it.

Also, Kate remarked that the photograph in my textbook of condensed chromosomes that are dyed with florescent dye looked like glowey worms having a party as opposed to, I suppose, the un-condensed chromosome illustration on the cover of the textbook, which she said makes her think of spaghetti (and now I'm hungry and will need to go look for food afterwards).

(You know, I was well into high school by the time I finally learned how to spell "spaghetti." The "h" in the middle always confused me because I'd remember that there's a silent "h" but never quite remember where to stick it.)

But the brief thought on genetics reminds me of one of my professor's comments today, where she said that "breeding is like evolution on Speed." There were smiles all around for that. And the TA can't count, but that's alright, the professor's not the brightest with math either and she's very good natured about it and so I don't believe he'll suffer from his mistakes.

Which reminds me that I've made yet another spectacular mistake with negative signs yesterday, so I shouldn't be talking about other people's math skills at all.

Probability seems much friendlier in comparison. No negative signs.

A morning lost

The adoption fair for FFO this week has been shifted to Sunday and, after some consideration, I've decided that even though by technicality Sunday should present no more problem than Saturday, I would really hate having it (permanently) on Sundays.

Why? Because Sunday morning is the only day of the week where I feel comfortable sleeping in a little. Because Sunday morning is the time(my time) between finishing everything that's due on Monday and trying to get a head start on studying and prepping things for the next week. Because, in a sense, Sunday morning was peace.

Have you ever had a morning where you woke up completely relaxed, with your mind gloriously warm and blank while you stared at the light playing through the curtains? It is those few moments before your memory and your conscious (and your guilt and whatever else) kicked in -- those few blissful moments. I get them on Sunday mornings and, unless drugged, no other time. One summer when I was in high school I'd taught myself how to remember my dreams (enough to record them in detail the next morning) and to wake up instantaneously -- and had spent three consecutive months afterwards trying to forget how. Immediate wake up, I've learned, has it advantages, but it usually means that you can't go back to sleep afterwards, either. (Your day begins with your first moment of consciousness because you'd unthinkingly replaced the dial switch with the on / off switch.)

So Sunday morning is my moment of peace, and as much as I want to do my best for my foster kitties, I really would resent their intrusions into my Sunday mornings.

And no, my personal definition of peace is not just that moment in time. (Heavens forbid me from being so sensory deprived.)(Joking. Sort of.) Peace is more than any sort of a physical, sensual thing -- even the personal kind. But peace, like many other feelings, is something that can be triggered by physical, sensual things. It can be stored in things around us the way memories can, and so I say that peace is also the sound of rain on pavement and the smell of jasmine, tea or otherwise. World peace and political peace definitions aside, peace is also a sort of calmness, which I like to link to the image of the ripples on a quiet pond.

Peace, I think, should be a sort of pale, sage-green -- something cool and comforting that you can wrap around yourself at the end of the day.

I wish I could say that I have as good of an idea for happiness as I do for peace, given the two are, more often than not, inclusive. I do have some ideas of what it might be (and it would be more than the fireworks of laughter and ice cream -- so bright, but never lasting). What comes to mind when I try to pin it down in wiggling, tricky words is a series of snapshots (because I can't help thinking in pictures): sunshine on grass, home with the cream-colored futon and calla lilies, Borders the day after Thanksgiving. What I have are the lit lamp by the door when I come home late after a meeting, a cat purring by my feet where I sat in the dark (and so many other photographs that I try unsuccessfully to juggle together, like a puzzle with pieces still missing). It doesn't quite fit yet but one day, when it does, I'll let you know.

I do know that I think happiness should be the color of amber -- the warm honeyed hue with just a hint of gold.

And now I think I'll go and scrub out the bathroom. Excuse me.

一千只荧火虫

开学后第一个正式上课的礼拜过的比较忙碌. 每个学期都是这样, 何况这个学期又是本学年的开始, 所以乱七八糟的事更多的不用说了. 再加上点报大学的事 - 我应该为我这个学期少选一门课而感到欣慰.

总而言之: 地一周 = 俱乐部 + 买书 + 找教室 + 试验室安排 + 其它没有想象到的事(生活中充满了这些). 谢天谢地第二周的事相比来讲少多了.

妈据(她的电子邮件)说已经到了302, 并对时差感到困惑. 我只记得在有夏时制时北京的时间是美国的时间(12尽制)加三, 然后把黑白颠倒(这的白天等于那的黑夜). 没夏时制时要加四小时. 当然虽然说的容易, 每次我也得想那么几秒中才能推算出正确的时间.

复习继续! 大学的事在收到考试分数后正式开工!

A few words on chemicals

I've encountered many discussions (well, more than usual, anyway) about organic vs. inorganic things lately. It's not just food, because I think we can all agree that THAT discussion is getting a bit over-discussed now -- most people just settle for their view points and use the so called "discussions" not to listen to other people's opinions, but to browbeat others with their own. No, I'm talking about the other things -- the food additives, the pesticides, and so on. For the records, these are my thoughts on the subject matter:

Organic isn't always "safer" than inorganic. From what I can understand of it at least, many inorganic substances are easier to analyze, without the complicated mixture that permeates every single organic extract. You can get an inorganic food additive that may be safer than the organic kind because of the things that might show up, mixed in with the organic compound that you want. Inorganic poisons are effective, yes, but keep in mind we have some pretty effective organic poisons too -- mother nature, after all, has had a longer time to study chemistry than you and I. Taxol, for instance, is a cancer drug that is essentially a form of poison. It affects microtubule organization in cells and thus inhibits cell division. It's also an extract from yew trees. Foxglove extract is used as a vasodilator but in its more concentrated form will cause your heart to stop and no -- they are not there to poison us on purpose, they have these things in them to prevent themselves from getting chomped on by herbivores looking for a yummy green snack.

In other words: no, I don't think organic things are the miraculous cure-all harmless things that some people seem to think they are.

However -- and make no mistakes about it -- I am for the organic things. As I've said, mother nature has been at it for a longer time than we have, and has created, for her class projects, things of unimaginable complexity. For every single thing she has created that can be considered a poison, she has either an antidote or some other ways of take care of it. A dead foxglove, for instance, will not poison the land it was growing on. This is in contrast with many man-made chemicals that has no counter parts in nature and so can't be degraded or countered or whatever (DDT and diedrin come to mind). These things stick around and can't be reused and believe me when I say that our chemical garbage is kind of a big problem. Plenty of chemicals are as effective at causing mutations as radiation. Nature can clean up after herself. We are starting to learn how, but learning something is not exactly the same thing as doing it.

People buy organic food for this reason, though not everyone knows it. Organic foods don't have inorganic pesticides and growth hormones because those things are man-made and can build up in our bodies in lethal amounts, given enough time and exposure. But -- and I will repeat this -- people also shouldn't just assume things are fail-safe and fool-proof (personally I'm of the opinion that nothing in this world is truly fool-proof, anyway)just because they're labeled "organic."

My suggestion? Being an informed consumer. It's good for your body, it's good for your mind (in fact, you can go and impress people now with what you've learned about microtubules -- they are essential for cell division).

On a side note, organic phosphates in pesticide/herbicide/whatever doesn't actually mean it's derived from plants. It means organic in the sense of organic chemistry. The things that are considered "organic" by the common definition is usually listed as extracts of this and that.

The fuzzies

Last night was an event that reminded me of why I thought fostering only one cat (until Annie came back) is a good idea.

I had a busy day yesterday, being stuck on campus for nearly eleven hours. Simba wasn't very happy with me because of that and also because once I got home I didn't have time to play with him (the horror of horrors!) and then, to add insult to injury, I abandoned him (when I've already neglected him) to sit with the Scary Black Thing in the other room. Yesterday was, consequently, the only time in my history of fostering him that he scratched on the door for five minutes after I went to bed. Usually I get about two seconds of noises in the morning to let me know that he knows that I'm up and so would I please come out and pet him? But no, yesterday was scratching and whining after I closed my bedroom door for the night (and he knows it -- the benefits of being a scheduled person during socialization turns out not to be not so great a benefit during fostering).

Then of course, Lucy isn't happy with me at all. She stomped a lot last night and when I went in to check on her she just stared at me balefully. I got the distinct impression that she was blaming me (through no fault of my own) for Kate's disappearance. I was woken up this morning by the sound of rabbit teeth attacking wire cage, which was loud enough to be heard straight through the walls. Feeling somewhat peeved and -- alright -- vaguely guilty, I got up, went over, opened the window, fed her, and petted her, thinking that this might calm her down a little. She bit me, which promptly put an end to the petting session and any desire to let her out of her cage this morning. Socialization has taught me that I shouldn't let an animal out of its cage until it's comfortable with being petted inside of its cage (and Hippo had looked scary back when he hissed at me -- he'd hunker down in the corner of the cage, where it was dark, and the only things I could see would be the two yellow eyes and lots of white teeth). It would be funny if it turns out, in my entire experience of dealing with socializing feral cats, that my only scar is the result of a house-broken (sort of) rabbit. I wonder if this can be used as an advertisement for how tame our socialized kitties are.

Lucy is still making a lot of noise this morning and so, since she's shifted from staring to glaring, I bribed her shamelessly with her treats. Though, considering her reaction to my fingers, I probably will not be sticking my whole hand into her cage any time soon. I will make another attempt later with cranberries, though if she still hates me by Saturday Kate'll have to clean out the cage on her own.

Of course, all of this is taking place with Simba crying piteously outside of the door (just imagine what it'd be like having two cats simultaneously wailing!). I heard a loud thump from the living room area last night, but further investigation, coupled with watching his antics this morning, has forced me to conclude that it was probably Simba falling off of something while he was pouncing.

Ah, there's the stomping again. My cue with cranberries on top. Heh.

[edit: 10/6 13:46]
Lucy hates me.

In which biochem wins again

I woke up this morning in the mood to write, I thought, a passionate yet logical essay about conservation biology and some of the dangers our current ecosystems are facing that many people aren't even aware of. It was not the sort of mood that I can swap for fiction-writing mode (sorry, Lucy), nor was it the sort of thing that's a precursor to scientific papers. It was ranting, albeit a slightly more coherent kind.

I was in the mood. I was in the mood during breakfast, still in the mood while I changed the cat litter. I paid attention in plant genetics and thought about how to incorporate what I was learning into my argument ("when it comes to the environment humanity often behaves like a spoiled child - making a mess without a thought about how to clean up after itself afterwards"). I formulated the paragraphs in my head during lunch, concluded I had some time in the afternoon where I could nip over to the computer lab in Hutchinson hall, and thought I had at least enough time to type up a basic rough draft.

Then I had bioenergetics, and I couldn't think about anything except enzymes for two hours afterwards. Metabolism does that to you. The thought of enzyme is like a incipient bacterial disease: at first there is just barely a thought, lurking insidiously in the back of your mind and then - quite suddenly - they're EVERYWHERE and they crowd out all other thoughts until all you can think about are aldose ketose conversions and why on earth there are so many "ases" (enzyme names always ends in "ase", e.g. kinase, isomerase, etc.) around. Thoughts about the paper and the environment were pushed out. I tried reading an environment-related book for a while but that produced no result except an almost irrepressible urge to lie down and take a nap somewhere. There was no doubt about it - my mood was ruined.

Which is why I am not writing a rant on environment today, after all.

And apparently Kate is still reading this. Hi Kate!

At least they don't scream

Classes continue and I seem to have acquired this week, along with some formidable reading assignment sheets, a huge number of notes and handouts that I have to print. I am not complaining, mind you. Even if I use up one ink cartridge per quarter (which has yet to happen, even with the considerable abuse administered by the communications & ethnicity class I took last fall), the cost is still considerably less than it would've been had the teacher, say, insisted we buy a supplement book (which does happen for some classes).

The printer is slaving away, even as I'm typing this (and the table is shaking because of it). I think I have over 200 pages to print this quarter (some of which I can foster off of the campus printers) (60 sheets, to be exact, as the student account so loves to remind me), but even so, it's still sadly more economical than the cost of textbooks.

Speaking of economics, Lucy, you would've liked my plant anatomy class' TA. He is tall, somewhat dorky (okay, very dorky), and warned us on the first day of the lab that he will be telling us lots of bad jokes. He overheard me mourning over the coleus plants today (after we make the incision for two of the treatments we have to remove the head of the plant as well as all leaves, so I was remarking on how sad the plants looked) and he commented that at least the plants don't scream. Which made me twitch, just thinking about it. He also said that if we forgot our lab equipments we can borrow our partner's, since that's what lab mates are for - and then he promptly started singing something that along the lines of "that's what mates are for" while the class looked on with baffled amusement. (And no he's not British.)

Simba attempted to climb up my leg today. I discouraged him firmly, but I doubt it will register in his furry little head. There is a flavor of the myth of Sisyphus to trying to train a cat.

三步曲

上周末回家, 考了GRE, 所以可算又完了一件事. 通报了家长和KATE我有可能今年毕业. 总的反映还算不错, 没有什么特别神经悉悉的. 现在已经是另个礼拜了, 所以又该忙着些其它事了.

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Here are the signs of another school year starting: increase of population in Davis, bikes going wrong-of-way, and random people stopping you to ask for the directions. The most common destination I've given directions to, as far as I've kept track of, is the Silo where students can go and, for five bucks, get the sort of fastfood you'd expect to find located near gas stations on interstate highways.
The runner up is the arboretum, but then, this is Davis. The Silo directions are more often asked anywhere on campus and the arboretum directions are only asked if you are near the southern part of campus, but the arboretum directions are harder because it's a larger place and the people who are inquiring about it usually can't tell you which part of it they wanted to visit (Is it the headquarters? The Redwoods Grove? Putah Creek Lodge?).

Here are the signs of another school year starting: backpack checkouts outside of the bookstore instead of tiny backpack lockers in the bookstore, freshmen traveling in packs (who said that civilization's removed our evolutionary instincts?), and fraternity/sorority flyers everywhere. The clubs and the religious groups have their own solicitors, of course, and I plead guilty to designing the flyers for Botany Club. On the long run, however, the clubs and religious groups are mauled down and forgotten behind housing ads and last-minute "roommate wanted" signs, while fresh frat/sorority flyers appear miraculously appear on top of the bulletin build up every other day. Their sort of dedication borders the fanatical, but those who had to deal with the drunk members - well, we already knew that anyway.

Here are the signs of another school year starting: the last minute construction designed to finish just the day before school started, on the spot peer-to-peer training at all stations from the library check out desks onwards. There are the few roller backpacks before the students find out that roller backpacks are not the way to go in Davis. There are the cranky students, me included, complaining about the cost of textbooks.

And here it is: just one more day before instruction begins.