20071124

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.

20071117

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.

20071114

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.

20071113

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.

20071110

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.

20071108

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?

20071105

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).

20071104

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.

20071102

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.