A mischief of mice

So I'm working on nine different experiments right now and the PI has come out to talk to me about the NRSA (f31) fellowship and hinted strongly that I should get myself registered now and apply for the one this summer. Also, he thinks I should have an undergrad. I was personally considering separating out the teaching part of my learning experience from the research part of the learning experience because 1) there're only so many things I can focus on on any given moment, 2) undergrads come in a variety of competence -- the good ones are excellent, but occasionally we do get people who come in, after their freshman year of chem and math courses, and needs help figuring out how to dilute something one to ten and those...are time consuming and there's no guarantee which undergrad will come into which lab and also, 3) if nothing else, doing more teaching-related stuff later will give me a larger age gap between myself and the person I'm teaching. I didn't much like working with undergrads when I was an undergrad (with a few notable exceptions), a fact that I pointed out to the PI (he was amused), so I'm hoping age will bring wisdom and patience.

Then again, it is possible that it will be like my relationship with the average high school student -- beginning with vague feelings of alienation and ending with confusion increasing exponentially per unit (years) of time.

Lost another litter of mice to the parents. The crazy crazy inbred cannibalistic parents.

My new computer was supposed to get shipped on Tuesday, but due to the processing time of the order, the processing time of the money transfer, and the processing time of the order for airplane tickets for Greece, the keyboard protector was able to be processed and indeed, I received it today, but the computer order wasn't processed and then they cancelled that order. I managed to sort that bit of fun out, but now the computer isn't due to be shipped until next week and Ivy is having a particular glitchy week where it freezes randomly when I have the browser and multiple files open at the same time. Zen's...well the OS is stable for NOW but there's something very wrong with the fans that I'm very, very clueless about (which figured because the original problem started because of overheating, if the error message is to be believed). So now I'm not even turning on Zen at all because the noise from the fan makes me fear for my personal safety. As in I'm worried about overheating and melting things and possibly the battery exploding (it's lithium). So, well.

There is brominated vegetable oil in my citrus soda. And at some point I need to mail someone in another lab about Bermuda land crab, or at least its cDNA. And I need a new long sleeved shirt. And more sleep.

My yokan tastes of preservatives. It's not helping with the paranoia. Though I have figured out at least one reason why one of my experiments was not working: the antibody I used is one that is conjugated to an enzyme and the enzyme in that batch is dead. I got a new neighbor on the other side now, and the first night so far is pretty good. I need my new vaio to come in soon so I can install the printer/scanner software somewhere or to mess around with wine again in linux (and possibly finally learn pearl except that's not going to happen due to the lack of time) and oh right, I was told that it's Easter. Happy Easter?

Frustrated ranting: you have been warned

On Daemon. Lackadaisy's signed poster has arrived, thus improving my day. No result for experiment yet (ten-day protocol/procedure is INSANE). Anything I need that MIGHT fix Zen requires purchase of frankly expensive bits of diagnostic software (ah the Windows market-lock) -- can't find immediate open-source solution for software-hardware interface issues in XP, if those are indeed the issues, ended up wiping Zen (all files are gone anyway -- I never exported or backed up my playlists, darnit) and replacing with Ubuntu, since linux tools are always free. Currently can boot up and everything but system will occasionally do very odd glitchy things (software program only, nothing so scary as blue screen of death or "20% of RAM is usable") but are nevertheless v. annoying. No time to do more right now. Failed to use dA mural there because glitchiness, though tablet still works well as mouse, nor can I draw anything digitally right now (woe), so that's a total wash. I need a plug-in for real-player files as well now because currently ALL my computers are linux and I need one (non-glitchy) computer than can still handle all the locked file types.

Tried to buy a VAIO today and failed. Can only directly purchase (as of now, still waiting to hear back from this one person) stuff from Bookstore, Bookstore only has two very old models of VAIOS that the sales people DON'T EVEN KNOW if they have integrated mic or not, or the length of battery life (not on "spec sheet" -- a laughable 5 by 8cm piece of printed card-- at the store, or on pricing sheet at the store; those models no longer can be found on Sony's website so it required going back to lab and looking them up elsewhere and my God that amount of time could be so much more profitably spent elsewhere), and Bookstore don't do "special orders" for Sony...or half of the other PC brands there, so you can't order a newer model THROUGH them either. They do do special order for Dell, but there's currently no Dell at the weight / size that I want that has an i5 processor, much less the battery life. Lenovo has a bunch of issues though they do have nVidia graphic driver (shiny!) but ultimately those things are HUGE and rather hideous in design and why is buying a laptop I've already picked out online with funding that's already been approved and paper-work'ed so difficult, anyway?

Going to bed early. It's that sort of day.

Forgot to turn off Zen before leaving for lab. Returned in the afternoon to use it and had it crash on me. Current report is that RAM overheated and only 20% is usable, with 64% of harddrive being still accessible. Have no access to any program besides Firefox & Windows explorer. Lost all files that were not backed up (including all my recent sketches and art projects but thankfully nothing academic). All the software / OS checked out intact as far as I am able to see. Short of reformatting everything there is nothing to be done at this point. Despite of the fact that I have gotten an "okay" from PI I still have not sorted out the paperwork with the funds manager and the VAIO that I have my eyes on is already on backorder to April 26th (it really is very shiny).

Yes, Ivy is still suffering from occasional glitches.

Yes, that means my most reliable comp power right now is Daemon.

Dammit. This is spectacularly bad timing.

It's world lab animal libration week next week

It's hard enough to do biomedical research involving live animals without having to worry about bomb threats from activists, thanks very much.

Though I wonder if it is really as world-wide as they claim. My God -- can you imagine someone trying to "liberate" the lab animals from research in Egypt? More confusion! Or perhaps it is confusing enough over there that this is a small enough bleep that it won't even register on the radar....

[edit 8:24]
Forgot to comment on this XKCD comic. Or more precisely, how much it reminds me of my PI, since abuse of statistics (which, sadly, you do see in journals, even the higher tiered ones) is one of his favorite pet peeves. For historical reasons we use 0.05 as cut off and for basic tests, that's fine, but when you are testing a large number of hypotheses...well 0.05 is still a 5% chance of false positive, which means you'll find a "significant" result in one in twenty tests just by chance. (And why are they not using ANOVA, any way?) An example in my field, for instance, is testing the linkage between a certain allele of dopamine receptors and...say schizophrenia. There are different types of dopamine receptors. The researchers could start off by testing, say, D4, which they found no linkage. Lack of result = no publication and so, naturally they move on to test receptor D2...and so on. If they test 20 receptors (I don't think there are 20 types of dopamine receptors, but for the same of argument let's say they are testing all neurotransmitter receptors) there'll be one that's linked...if they test 40 there'll be two. If you repeat the 40 tests there might still be two that are positive, but it most likely be a different two because those two happened to be positive by chance. There are various ways to counter that. Bonferroni correction is the simplest and most commonly used for multiple-hypothesis-testing.

Also, yes, replication is important, technical replicates don't count (but biological replicates do), a minimum of 3 reps is good for the standards of most people, but our PI INSISTS on 5 reps whenever possible because of the robustness of stats. Scientific claims in popular news tend to give me headaches. Even pop-sci journals are better but alas, they don't have as strategic placement of splash pages.

Cream of potato soup is like clam chowder with out the clam. Or the bacon. There is onion involved though, and too much salt.

Have enough data for a manuscript but PI is going to have me try for a top tier journal which I DON'T have enough data for yet and won't until a particular experiment that I've been failing on and off since my first year works. He's also worried about being scooped. I would be lying if I said I am not a little stressed out by all this.

Am going in to lab both days this weekend again, but thankfully only a short stop each day. Tomorrow morning I plan to de-stress by spending hours along a street in the rich people district, where there are some very beautifully constructed private residences, and take reference photos for my practices at building drawing. With luck I will be unobtrusive, or at least innocuous enough in appearance, to avoid any possible wrath (and possible legal ramifications) from people who don't like their houses photographed. Then I will go to lab and then home and then it will be Monday again, alas, and I have just lost a little of mice together because they got eaten by their parents. They really need to stop doing that.

Declensions: 1; me: 0

Channeled Mike yesterday and ditched lab for an hour and a half to go to the Kyoto Prize symposium yesterday, to the one that was hosted on campus, which was the award for basic science. This year's basic science prize went to a Laszlo Lovasc, in applied math, specifically as applied to networks (he gave internet and neural networks as examples; I was gleeful). There weren't that many equations and he demo'ed an online program he wrote that everyone can play around with, whose url I left on the back of protocol sheet in lab. I'll post it later. It was fun. To complete the feeling I had a turkey salad sandwich for lunch, in which I was boggled to find pineapples. Which were not listed in the ingredients. I checked three times just to be sure. Dried cranberries? Yes. Pineapples? No. If they are going to bother listing the ingredients down to the preservatives (EDTA, yum -- I use it to de-calcify samples in lab) they really should list something that's rather large (it was in chunks) and noticeable, both in appearance (yellow) and taste (pineapple is hard to mistake). It's almost as weird as the quesadilla with the chicken-bell pepper-mango mixture, but at least that one had no lying ingredients section. I feel betrayed.

Had a discussion about ethics again (it's a quarterly requirement), specifically about ethics in biomedical research and the responsibilities of those of us who specialize in genetics. It has sucked all the enthusiasm out of my life. Or so it currently feels like.

Oh and for those who didn't know: Anna won the NSF fellowship! It's this hugely prestigious pre-doctoral fellowship covering your stipend and such. I've tried twice and wasn't quite good enough to make the cut-off but ohmyGod I have a friend who got it! Vicarious excitement is quite potent. Congrats Anna!

They have already plotted out the days for next year's Science Festival. Expo Day's March 24th, apparently, but this knowledge is a wee bit too early for me.

Last thing is the 3-D printing: I first heard of 3D printing via XKCD, about the tiny open-source violin and I thought -- okay, new technology, very cool, but ...can't really relate. Then Ars Technica ran an article today about copyright issues in 3D printing, I discovered RepRap and Fab@Home and suddenly it's sci-fi come to life:

Guy. Guys. You can PRINT a PRINTER.

Given the right materials, of course. Personally I was vastly amused by the range of ...uh..."material" that people tried (it's open source so you can try anything), from spray cheese to silicone to playdoh to metal to chocolate. There are commercial 3D printers too, and between the hobbyist and the companies people have printed everything from tea sets to synthetic muscles and just...wow.

Okay tired clean up then sleep.

At least I got jello

Monday: Wendy and I huddled together and wondered what will become of a research university when they cut all our research funds. Someone described my attention as a strobe light, and I finally got around to examining the shirt I test-tailored, which failed the exam since the sleeves that I had altered had not straight stitches on the inside complete with a few stitches where the thread twisted into a tiny loop next to the fabric that was not noticed / corrected and a missing stitch (not sure how this is accomplished as this was obviously done with sewing machine, but there's a place in the middle where the the evenly spaced stitch should go and it's just not there) (time to find up the next candidate then). I have spent around seven hours with my mice today. It's a new record.

Biosynthesis was a long time ago

My thesis advisor from my undergrad years just emailed to say that she's putting together something that involves the stuff I did for my senior thesis and she had a bunch of questions for what I tried and didn't try and since she's at home she thought that it'd better to email me rather than to check the records I left for her.

Dear all: this is from my work based on organism from another kingdom, involving the arginine - glutamine - glutamate pathway (huh, spell check will recognize glutamate but not glutamine -- why is that?) from three years ago. And I left 95% of my notes with her. Asking me to recite the passages from Hamlet that I remembered back in high school would've been easier. Asking me to diagram out the glycolysis cycle would've been easier. (They are one dimensional information, two at the most, but with your own data it's not just what and when, it's what and when and where and how and why down to the accuracy of less than 5% chance of mistake or else the final conclusion you draw will be wrong and this is why I chose to leave 95% of the notes instead of the usual 50-70%.)

O the frustration. I could weep.

Okay that's a lot of food

Parents came and parents left. After some consideration I've realized that parental visit this time around actually bore a striking similarity to the llama song (my God the llama song, I got it stuck in my head twice within a week of being introduced to it) -- in the sense that the first time you listen to it, after the 50 seconds of photos and inane lyrics flash by, you're left sitting thinking "What ...on earth just happened?"

They brought a HUGE load of food, asked me why I'm doing a PhD instead of a masters, I fed mom peptobismul (she was having stomach problems again), and I tried to update them on my life per their request (let's see...lab, lab, chores, lab, ooooh I volunteered at the Science Festival, that was fun, see this giant poster I have now? Nope, sorry mom, no boyfriend yet) while they randomly cleaned things. (I suspect that bring food & clean stuff may be in my genes as well, given their and my current tendencies, though so long as I refrain from procreating it may not get quite as bad.) It was good overall. Mom is flying back to Beijing in a few weeks and I confused both of my parents with the staple-less stapler. ("Is a card scanner?" "It doesn't require electricity?" "Is it a hole puncher?" "You can press down on it? What does it do? Did you just break it?")They brought over a catalog from "Bags and Bows" that they received in the mail because they remembered (!) that I like to flip through catalogs and occasionally I'd decide to keep one, and this one is definitely a keeper. It has patterns and color-coordination that is actually tasteful. I may have to start drawing Alice more so I can try to stick her in different color-theme inspired dresses.

Right. Off and about for the other stuff then.

But the world is...awesome

I saw this XKCD comic going around like a particularly virulent strain of influenza and started laughing, because Wendy is in the middle of putting together a manuscript for publication and our recent two weeks featured a two hour long search for the prettiest brains to photograph and, as of this week, a ten minute discussion on which of the two panel of five brains is prettier (and whether or not highlighting the folia of the cerebella contributes or detracts from the overall aesthetics).

(Personally I prefer immunofluorescence. They're shiny! And if you work in fruitflies and have a particularly good confocal laser microscope you can layer up to six colors per embryo!)

(Though I also think Trizol is kind of pretty, especially when you're at the chloroform layering step.)

So there you have it: beauty is in the eye of the beholder, and here in the fields of research, we're all a bit mad.