Russell's Blog

One of the wonderful things about web applications is that they can be available 24-7. They can sit there and quietly do their jobs -- taking orders, billing credit cards, assigning work orders, or whatever -- even when the office is empty. That's one of the main reasons one would go to the trouble of putting a web front end on something in the first place.

So, the question of the evening is, does the UC Davis registrar know this?

Um... no.

This is a completely automated process. If you do this during the daytime, it just goes ahead and populates a table in whatever chthonic legacy database system that is swaddled in this blob of early 1990's vintage web programming. It's not like having the office open at the time actually helps.

Attention Amazon.com shoppers! It's 4:45 Central Time, and Amazon.com will be closing for the day in 15 minutes! Please complete your order before the site is disconnected for the evening. We will open again tomorrow at 8:30 A.M. Thank you for shopping at Amazon.com!

On the upside, at least it doesn't complain that my browser isn't supported. Yay.

Now that I have a free moment between chopping potatoes and mashing them, I figure I should post the paper and talk I wrote summarizing my first lab rotation.

I tried to make the paper look like an PNAS article, but alas, their LaTeX template leaves much to be desired. I like how the talk turned out little better, thanks the wonderful Beamer package for LaTeX.

One of the projects I've been working on this semester is designing a teaching unit for the UC Davis introductory biology curriculum. The introductory biology courses are required for a whole bunch of different majors at UC Davis, so all three of them are offered every quarter. It's a huge effort, and thousands of students take these classes every year. This is part of a teaching seminar led by Scott Dawson (don't bother Googling for him -- you'll find the wrong guy). The idea behind Scott's seminar is to take the half-dozen or so concepts that the BIS2A, 2B and 2C students struggle with, design teaching units aimed at those topics, and then try them out on volunteers. My topic is stochastic processes, which has been great fun. The project isn't finished yet, so I'll save the details for later.

One of the other issues we've been addressing in the seminar is how scientists relate to non-scientists. This is, for obvious reasons, an essential teaching skill. Even if they hope to be scientists someday, students are not scientists. If you don't find a way to talk with them about science, then you're wasting their money and their time.

The idea that the educator is largely responsible for the success (or failure) of the student hasn't really seeped into higher education, although it's been the standard thinking in primary and secondary education for decades. Not all elementary school teachers are good at what they do, but it is generally agreed that if they are good, the results will be seen in the subsequent success of their students. In higher education, things don't really work this way.

The most often cited reason for poor instruction at the college level is that many professors consider teaching secondary to their research. While this is clearly true in many cases, teaching in higher education doesn't just suffer from playing second fiddle to research. Many, many professors (even whole departments) who take teaching seriously are nevertheless not very good at it.

There are two causes, both of which are systemic problems. First of all, people who teach at the college level are usually not trained as teachers. Many (most?) professors have no education training whatsoever. Yet, even if you have natural skills, teaching isn't something you can do effectively without at least a little theory and training.

The result is that most of the teaching in colleges is done by amateurs and autodidacts. In contrast, at the primary and secondary level, teaching has been a job for trained professionals since the turn of the last century.

The second problem, which is partly a symptom of the first, is regular old-fashioned chauvinism. It is the responsibility of the student to learn, but many professors fail to see how they fit into this. This might be acceptable at a private, endowment-supported institution, but such places are exceptions. The Harvards and Oxfords of the world are free to treat their students however they like, but public institutions are ultimately responsible to the taxpayers. The taxpayers support such institutions for two reasons; to conduct research, and to educate their kids. Sink-or-swim pedagogy is a dereliction of duty.

This is a problem that extends far beyond the classroom. I was listening to NPR on the drive down to Los Angeles, and caught a story on All Things Considered about the reception of Darwin's On the Origin of Species. Some extracts :

"That fraction of people who figured that they could and should keep more or less up to date with what was happening in geology, in botany, in zoology, even in physics and mathematics is a much bigger fraction than it is today," says Steven Shapin, a Franklin L. Ford Professor of the History of Science at Harvard University.

...

"We hear about scientific findings," says Shapin. "But the proportion that can evaluate them and follow along with them, as opposed to hearing about them, is very, very small."

Shapin says that since people can't be completely conversant with the relevant science, "They're looking for an answer to the question, 'Who can we rely on? Who's speaking the truth? Who can we trust?' "

I think the good professor is missing the point. The problem is not simply that science has gotten more complicated and technical. It is true that there is more of it, and that it moves faster. The reason I don't buy Dr. Shapin's argument is that this is not at all unique to science. Everything moves faster and is more technical now than in 1859, and people seem to cope just fine.

The problem is that scientists do not spend enough time talking with the general public. Only a small minority of scientists take the trouble to arrange their findings in a form digestible by the lay audience, as Darwin did. When they do, it is almost never cutting-edge research that fills the pages. Very few scientists go on television or the radio. The practice today is to bring research to lay the audience only when it is neatly tied up (or, the research community feels that it is, anyway). There are those who do otherwise, but there is a negative stigma to it; scientists who announce their findings with press releases instead of peer-reviewed papers are usually regarded with suspicion.

Darwin's target audience for Origin -- the typical educated Briton in 1859 -- would not have much of an advantage on the average American in 2009. A Victorian gentleman would probably have had better handwriting and more patience for trudging through elliptical turns of phrase than an American high school graduate, but I don't think they would have much of advantage when it came to comprehending an unfamiliar scientific topic. The advantage Darwin's audience had was that it had Darwin.

When a good teacher notices that a student is failing to learn something, they will look first at their own teaching methodology for the problem. The same goes for scientists; when the general public doesn't understand or care about a scientific topic, a good scientist should look first at how they are publicizing their work. If the public doesn't think your research is important, then either you aren't explaining it well enough, or maybe it actually isn't very interesting.

Looks like I got my gene to grow in E. coli!

The colonies that didn't get the plasmid I'm using to carry MXAN7396 turn blue when grown with X-gal (bromo-chloro-indolyl-galactopyranoside). The ones that got the plasmid don't.

Neat!

I finally got through the double-PCR phase of the protocol without wrecking something. Yay!

My hacked up version of the gene gene is getting snipped up with everyone's favorite restriction enzymes (BamH1 and EcoR1). Then I get to splice it into a plasmid, and electroport the plasmids into some cells, and maybe they will do something interesing.

I've been doing my first laboratory rotation in Mitch Singer's lab, and trying to learn what people are actually doing when they publish these spiffy experimental results. So far, I've mostly been wrecking things. Fun disasters of the week :

• Wrecked a DNA extraction by grabbing the wrong Pipetter and putting 300 microliters into a tube instead of 3.
• Misread an illegible label and used butanol instead of ethanol, destroyed second attempt at the aforementioned DNA extraction.
• Dropped the wrong tube in the trash, screwed up the third attempt at the aforementioned DNA extraction.
• Kept a gel on the UV bench too long while trying to chop out little cubes with a razor blade, annihilated all the DNA, and screwed up fourth attempt at aforementioned DNA extraction.
• The PCR cycler didn't close correctly, and my reaction tubes evaporated; screwing up fifth attempt at aforementioned DNA extraction. (At least this one wasn't my fault.)

I'm now spending the evening in the lab running everything over again, for the sixth time. Yays!

I definitely sticking to informatics -- that part of the rotation is going pretty well. I'm just not cut out for benchwork.

This summer has turned out a bit like a chocolate bar in the sun; everything started out nice and neat, but everything ended up squished into the bottom of the wrapper.

Right now, I'm working with Andrey Kislyuk on our little piece of the DARPA FunBio project. We're in the middle of a two-week code sprint, so I'll save that for a later post.

I also moved to a new apartment, and that didn't go nearly as smoothly as it could have. The guy we subleased from was in the process of buying a house, and the loan underwriter decided to yank back the money after he'd closed escrow (or was in escrow, or something). Evidently they wanted a sworn affidavit from the gardener that he was contracted to take care of the grounds. Anyway, the upshot was that instead of a nice leisurely move, he got stuck in the apartment for three weeks longer than he expected, and I was homeless for a week. Fortunately, one of the staff scientists in our lab was generous enough to let me stay at his apartment. Neil and Buzz got to learn about stairs, which they evidently adore.

Over Labor Day weekend, I went with Srijak and some of his friends from San Diego on a day hike at Lassen Volcanic National Park. I've always loved California, but it's nice to be reminded from time to time exactly why I love this place so much.

Because it's awesome.

This quarter, I'm taking :

• Mathematical Methods : Laplace transforms, Fourier transforms, Greens functions, and their applications to partial differential equations.
• Quantum Mechanics: Again. For the heck of it.
• Numerical Methods: Analysis of the performance, stability and error propagation of numerical algorithms in finite precision systems.

So far, it's way more fun than last quarter. Still, I'm disappointed that the molecular structures course I wanted to take conflicts with numerical methods. Hopefully I can take it next quarter.

The preliminary exam for mathematical methods is in the middle of finals week at the end of this quarter. That is going to suck.

When it rains, it pours! I've been hanging around all summer wondering what to do with myself, and now suddenly there is a huge explosion of activity. After a four day expedition to Davis to sign paperwork at Graduate Studies, register for classes, look for a job, look for an apartment, and get a sense of what it will be like to live here, I drove back to Los Angeles for my cousin Nathalie's wedding (Sunday) and my great aunt's 88th birthday (Monday). Both were beautiful. Then I packed my car and drove back to Davis this afternoon.

Tomorrow, I have a job interview and tour for an on-campus job working in one of the Department of Entomology greenhouses. Not quite as good as a TA position, but it would pay for rent and get me outside and moving around on a regular basis.

I still haven't found a place to live yet, but a very nice fellow from my department is letting me crash on his living room floor until I do. Classes were supposed to start Thursday, but evidently the professor for that course isn't here yet.