Impressions

The water dispenser outside my lab has a cold spigot and a hot spigot. The hot spigot dispenses water which is actually quite hot. However, I couldn't figure out how to use it at first... until I realized that you have to put the handle in a certain position, which is not its natural low-energy gravity-ordained position, and then press it. It's a safety interlock! Good thinking! *makes tea*

I drove in snow for the first time recently. Well, not snow, but there was some kind of sleet-like substance on the roads and falling (slowly) from the sky. It was also the first time I ever skidded (a small amount). I've been on a skid mat, but it was a while ago and I remember it very poorly. I think the problem with the skit mat was either that I was unable to actually skid, or that it made no sense out of the context of a street and the slight hazard of hitting parked cars. There's no spatial reference on an infinite frictionless plane, after all.

Plates of fermenting bacteria on a phenol-red containing medium have this wonderful tendency to grow into miniature sunrises (although they do develop a rather off-putting smell).

Figure 1: Like viewing the sunrise from a mountaintop outhouse.

I just reread Terry Pratchett's Going Postal, and I really liked it. He gives the sort of lovely far-off impressions of the world of the clacks towers that I want to go there but that might destroy the mystique -- you know, the same thing people always say about why the Silmarillion is written in such a dreamy mythic tone. And if Thief of Time is the Discworld's The Matrix, then Going Postal is its Jargon File.

I, for one, welcome my new bacterial overlords

Over the past 24 hours, and yes, I really do mean the past 24 hours, I've been constructing a growth curve in my lab. The idea is this: there's an easy way and a hard way to tell how many bacteria there are in a culture. The hard way is to take a sample of that culture, spread it out on a plate, and count the colonies by hand (assuming each colony arose from a single bacterium of the original culture). The easy way is basically a more sciency version of "just look what color it is".

Figure 1: Shall I compare thee to a summer's day? Thy color is more lovely and more linearly related to the pH of the solution. [Source]

The bug I'm working with ferments sugars for a living, so as it grows it makes its environment more acidic. This is really handy, because we have wonderful molecules like phenol red that change color according to pH. In this particular case, yellow means acidic and red/pink means basic, so as the bacteria grow, the ratio of yellowness to redness should tell us something about how long the cells have been growing and how many there are. Here's a paper by another group that used this method, although they did so much other (amazing!) stuff that you'd have a hard time finding the details (look at figure S4 on page 41). So it really does boil down to "just look at what color it is", except that if you need to be precise, you use a spectrophotometer instead of your eyes.

The trouble is that the yellow/red ratio doesn't actually tell you anything about the number of cells in your culture, unless you take the trouble to do it the hard way and the easy way at the same time and figure out how they correlate. This is called doing a growth curve, and it's something that has to be done for every different bug if you want to measure it by any method that's easier than counting spots in a dish the day after you wanted to know.

So... while I can't say I have been in lab for the past 24 hours (I took a couple hours off last night to go get food and a nap), I have been running this same experiment for the past 24 hours and taking samples more or less every hour. It's tiring in multiple ways. I could barely make myself come back from my dinner-and-nap break because I was in physical pain from being tired. Also, having to go do something for 15 minutes out of every hour is hell on your ability to get anything else done.

When I said I had blocked out the entirety of my IAP for this research position... I guess I really meant the entirety of my IAP. All hail science!

Lab Resolutions

Last summer I had an undergrad research position (UROP) in the lab of Tom Knight, one of the founders of synthetic biology. It was pretty good, but I really didn't make as much of it as I could have.

Then I went incommunicado for an entire semester. I just dropped off the face of the planet, as far as TK was concerned. Taking a break from research for a semester is not in itself terrible -- if you have a difficult course load, you have a difficult course load. However, just dropping off the face of the planet is highly unprofessional and not recommended.

In about half an hour I'll be in a meeting with TK, beginning my re-entry into the lab. There'll be random technical detail updates to go over... but privately, there are a lot of things I want to improve about the way I approach lab work. Thus, this list of resolutions, which I'll be periodically updating.

Scheduling / Productivity

- I will filter my internet access while at work, both WWW and zephyr. (I already have filtering mechanisms; it's just a matter of applying them strictly.)

- During IAP: I will go in to lab every weekday, and if I miss a lot, try to make up a bit on the weekend. Once term starts: I will schedule blocks of lab time among my classes, going in at least 3x a week... I'm undecided about the weekend. I will adhere to this lab schedule as if it were a class schedule, i.e. no skipping.

- If I didn't pipet something or run a gel or look at my cells or do any other Real Lab Thing, it didn't count as being in lab. (I'm not sure about this one... probably needs some caveats about "what if I'm waiting for my primers to come in the mail" or something.)

Communication & Stuff

- I will continue working on my M. florum project from the summer, and also discuss with TK what's best to do about the fact that I don't actually find it tremendously interesting. The solution may involve picking up a second project.

- If I'm having difficulty extracting some nugget of information from the literature, I will get help by the next day instead of putting it off. I will strive to ensure that said help actually improves my literature-searching skillz instead of being just "Professor Awesome saves the day again".

- In order to keep myself accountable for time management, and to keep a clear view of overall project goals instead of being bogged down in minutiae, I will have some kind of meeting or status update with TK every day I am in lab unless he's out of town. If he's out of town for several days running, frequent email updates.

- I will figure out a way of explaining my research to my relatives that does not include the word "plasmid" (and probably should not include the words "user interface" either -- last summer I got lazy and made up a computer analogy that wasn't very accurate).