Saturday, April 30, 2011

Bachelor Food

Tonight I dine on lentils, washed down with quaffs of white wine. For me, this is bachelor food, since tonight I am a temporary bachelor. The Real Doctor is away, and will not be offended. There's some dishes and wines that the Real Doctor does not care for, or loathes, but that I rather like. There's enough out there that we both like that I don't suffer from the absence of these dishes. However, if I am alone, I'll make them. So, bachelor food.

During a drive from Tahoe to Sacto, I asked Laurabee if she had such meals. She did--until Rad developed a liking for hers. Rad had some too, until Laurabee found out how to make them appealing.

I don't think the Real Doctor will learn to like lentils and Sauvignon Blanc anytime soon. Do you have a bachelor meal?

Friday, April 29, 2011

Friday Flora

It's getting to the peak of wildflower season out here in California. We haven't been out to see much of them, on account of all the excitement with moving and such, but fortunately we have some wildflowers in our backyard. Here's the exceedingly common but still very nice blue eyed grass:
And something more exotic--White Blue eyed grass, from my Mom's garden (which is better than yours):Blue eyed grass is close to being a weed--the flowers in the first picture are a volunteer plant that sprang up in a crack in the pavement in our yard. It's actually a member of the iris family. In addition to the blue and the white varieties, there's a yellow variety (I suppose it has hepatitis, or is perhaps related to the Cmdr Data on Star Trek).

Thursday, April 28, 2011

PIMBY (Please--in my back yard!)

Today's lecture in Bis2A is about the carbon cycle--how living things are responsible for taking in carbon dioxide and converting it to wood and flesh and ultimately fossil fuel; and how living things are responsible for taking wood and flesh and fossil fuel and converting it back into carbon dioxide.

I opened up the newspaper of record this morning and found an article about irate New Jerseyans, upset that their utility company had put unsightly solar panels on their telephone poles. I have to admit that I was a bit annoyed at the Jerseyans, much as I am annoyed at students who don't balance their equations. Hopefully, most of my students know that there's no free lunch: if you want to reduce carbon dioxide to biomass, then you need to oxidize something else and also put some energy in. As I tell my students, the second law of thermodynamics always wins. The solar panels in Jersey are reminding us of the same thing--and apparently, that reminder is upsetting.

If we want to solve some significant problems, I think we need more such reminders. When I get in a car, I make a point of telling myself that wanting to drive somewhere is the same thing as wanting more carbon dioxide in the air. I still drive, but a bit less. This blog post accounts for somewhere between .5 and 7 grams of carbon dioxide being added to the atmosphere--so, perhaps I should visualize a smallish lump of coal being burned, and also a small amount of a removed mountaintop and an acidified stream.

Or, perhaps, I could visualize something nicer. Unlike the folks in Jersey, I'd love to visualize a solar cell, but I don't have that option. However, I don't have to say that by wanting this blog, I want more atmospheric carbon dioxide. Our house is part of SMUD's "Greenergy" program, so a chunk of our power comes from the giant wind turbines I can see in the Sacramento delta.

But there is still no free lunch--by wanting this blog, I want a higher number of dead bats and migratory birds. The second law of thermodynamics always wins.

Friday, April 22, 2011

Alea jacta est!

The big deal in my life right now is that the Real Doctor and I (and Opal and as yet unnamed) will be moving this summer. I find moving traumatic, no matter how necessary it may be. I know enough of the Four Noble Truths to realize that the cause of this trauma is attachment, and that I need to let go of things, but it's still hard when those things have personality.

Last Sunday we said adieu to our yard chooks; they've gone to a new home with one of the Real Doctor's coworkers, and are busy finding their place in the existing pecking order. So, here's some last pictures of the girls, as they were bundled into a carrier and greener pastures. Goldie, the gold-laced wynadotte:
and Rosie the Rose comb Leghorn with Barbarella the Barred Rock:
I've already started missing them; I was ripping up some weeds in our overgrown backyard and found a big, fat, juicy, green caterpillar. I'd picked it up and started walking towards the coop before I realized that there would be nobody to fight over it.

Ave atque vale, birdies.

Friday Flora

I've got a backlog of nice plant photos--so, we'll go with a "My Mom's garden is better than yours" photo:So there! And if you don't believe me yet, here's another:

Thursday, April 21, 2011

Busy insects

These structures popped up overnight in an outdoor hallway of the bio sciences building.

They're chimneys of mud, made by soil termites. It's supposed to be a sign of rain, or of spring, or of bored termites (depending upon who you ask). Here's another view.
They're not very tall, maybe six or seven centimeters, but I was still impressed. The nearest exposed soil is a long way away, and I would not have expected that a wee beastie would be able to find a space in the seam between a concrete path and a wall. But nature will find a way, and it seems that the smaller the beastie, the greater the patience. (what's that, Opal?--Oh, Pomeranians excluded!) A close-up shows the construction of these termite towers of Babel--not baked brick, but little pellets of mud, chewed and regurgitated and cemented in place by termites.
I wasn't able to get a good picture of the builders. They would climb up only far enough to wave their antennae at me, then disappear before I could get a picture. I spent five minutes crouched awkwardly in a narrow hallway outside of a building full of scientists, and a half dozen people squeezed by me. Only one of these people (who I would hope are curious by profession) stopped even briefly to look at what I was doing. He got down to look at them too, and was delighted and impressed. I think that's the right response, and I dearly hope that my students would pass that test.

Wednesday, April 20, 2011

Education: yer doing it wrong

Like all classes here, my introductory bio class has a website and a chatroom. The chatroom is a pretty useful tool--the students use it to exchange information and ask each other questions, and I pop in every so often and answer questions too. Sometimes, though, it lets me see just how dopey students can be; here's a (summarized) example of what I found on the chatroom this morning:

(name withheld): how many quizzes can we miss?
(name withheld, again): did anyone actually read the entire 17 page assignment for today? [note--they've had about a week] I was up all night playing Portal 2 [note--a just-released video game], could somebody give me a summary before 3:00 PM today?
(name withheld, digging in deeper): By the way, there's a meeting of the StarCraft [another video game] Club tomorrow night, everybody come!

Tuesday, April 19, 2011

Perhaps not the best choice of words...

We'll do this in the manner of Carnac the Magnificent and Jeopardy, answer first.

a) a powerful new laxative
b) a new antipersonnel weapon
c) a string quartet
d) an over-the-top zombie/slasher flick

The question is "What did the Boston Globe critic Jeremy Eichler describe as 'viscerally explosive'?"

More on this later.

Wednesday, April 13, 2011

What could possibly go wrong with this plan?

First, go to the dentist. A bit of recent anxiety and some rather old fillings and especially crevice-y teeth meant it was time for "drill, baby, drill."

Then, while I'm in town, go to the bank to deposit a check. My mouth is still floogled up with anaesthetic and my tongue won't work well, so, just present the teller with a note.

Well, everything's cleared up now, and hopefully I can get back to slightly more regular posting here.

Monday, April 4, 2011

Monday Musical Offering

Finally, the finale:

Bach: Italian Concerto, 3rd movement. I'm not totally happy with my playing. This movement is fairly straightforward, with only a few really awkward bits. However, it's really fast. You can pretty much tell the point at which I stop imagining that I'm a violin soloist and come to grips with the reality of being an overmatched pianist. Oh well--I hope you don't come here looking for pianistic profundity. As noted in the video, there are other better players out there. I was surprised to find myself really liking the way Angela Hewitt played this movement on her Hyperion release. Normally she leaves me cold, but this was quite spirited. Also noted on the video--avoid Glenn Gould's version of this movement. It's just too fast.

Friday, April 1, 2011

You get what you select for

Selection is a stunningly powerful force. You start with a large and varied population, select a small percentage of that population based on some heritable characteristic, let the selected winners increase, and repeat with greater stringency. The results--whether it's natural selection, the force that Darwin invoked to generate all of life's diversity, or artificial selection, which humans unwittingly do to breed antibiotic-resistant superbugs--can amaze and confound.

When I was learning how to do genetic analysis, I was cautioned that "You get what you select for." This can be nice. To use an example from my postdoc, if you're interested in how bacteria "smell" their environment, you can create a large and varied population by taking trillions of bacteria and mutating the heck out of them. Then you can use selection: if you want bacteria that can no longer smell a particular substance, you only let the scent-blind live--all the rest you murder with antibiotics. Repeat this a couple of times, and in a week you'll get a large population of bacteria unable to smell. You can then study those guys and write a bunch of papers and become famous for understanding bacterial chemical perception. You get what you select for, right?

You absolutely get what you select for. In this case, you can tell if your bacteria aren't smelling something because they don't swim away from that substance. You kill the ones that do smell it with antibiotics. So, you have selected for non-smellers--AND non-swimmers, AND those that are spontaneously resistant to antibiotics. Worse, there's only one gene that you can mutate to eliminate the ability to smell that target substance--a very small target for mutagenesis to find. However, there's about 5 genes that can be mutated to give you antibiotic resistance, and dozens of genes that can be mutated to give you an inability to swim--a much larger target. So, you think you're selecting for inability to smell, but you're REALLY selecting for a bunch of different things, and you get what you select for--almost all the cells you select will have a swimming defect.

I'm reminded of this again and again, most recently by what's been happening with the public schools in Washington D.C. The schools were doing very poorly, with many students performing far below grade level. An aggressive superintendent came in, urgent to shake things up and demanding results. A perrenial question in education is how best to measure results--in this case, learning progress was measured by standardized testing. So, the new superintendent selected for improvement in standardized tests.

This was not exactly like genetic selection: teachers and administrators bringing in low test scores were not killed, but they were terminated. Those who brought in ever-increasing test scores kept their jobs and received bonuses. New teachers and administrators were brought in, all subjected to the same selection pressures. Over time, the population of teachers and administrators in the D.C. schools changed.

Well, you get what you select for. The superintendent did not select for improved learning. She selected for higher test scores, so that is what she got. It seems that teachers and administrators tinkered with the standardized tests--edited them after the students took them, changed lots of answers, corrected them, to produce the desired result. Others just gave their students the answers as they took the tests. Those who did were selected for with continued employment, awards and bonuses; those who used more ethical but less immediately effective means of changing test scores were selected against.

Selection is powerful--often more powerful than we can appreciate. The creativity of nature, when asked to provide a solution to a selective challenge, never fails to amaze and confound. We should not be surprised when the creativity of human nature comes up with similarly confounding solutions to selective challenges.