Protein reflections

We’re working our way through the major kinds of macromolecules in my Intro Cell Biology class — Carbohydrates, Lipids, Proteins, Nucleic Acids. Today I taught on the composition and structure of proteins. I really like the topic because it’s a chance to bring in so many of the concepts we’ve already discussed, like hydrogen bonding, polar vs. non-polar molecules, etc.

It’s also a topic that has been taught thousands of times before. A quick search on YouTube reveals hundreds of short videos, some of which are quite good, covering the same material. Yet there we were, talking about the same things: amino acids and peptide bonds, tertiary structure and protein folding. Why?

As best as I can tell, it’s because there we were, all together, all thinking about the same thing at the same time in the same place. Some of us understand more about it than others. Some have questions about it. But we all had made a commitment to be there with each other with the shared purpose of learning about proteins today. And I think it worked.

Getting back into the flow

I’m starting to at least think about getting back into the flow after a few weeks away from the usual schedule. At the end of July I spent about a week at the annual meeting of the American Society of Plant Biologists, which was a great meeting for me this year. I heard lots of great science and got some excellent input and feedback from people I respect and admire. I also met a few new people and have some possible collaborations simmering now.

Since returning from the meeting, I’ve been mostly relaxing and taking some time away from the office. I’m getting some projects done around the house and spending time with the kiddos as much as I can before they start back to school next week.

While I’ve been away, it looks like Fargo has been doing everything but sitting still. I used it heavily to take notes on lectures and conversations while I was at the conference, so I’ve dabbled with some of the scripts in my menubar. I’m looking forward to thinking more about how to incorporate it into my class this fall.

Handmade heat maps

Most of the day I worked on our poster, taking the opportunity to do lots of statistical tests to prepare for writing the manuscript, which comes next.

One of the comparisons I want to make is within a given treatment, across different time points. I’ve come up with a heat map presentation that I think I’m happy with, but I’m not totally sure yet.


In this graphic, green indicates a significant increase, while pink represents a significant decrease. I think this highlights the key points I’m trying to make, but I’m going to sleep on it.

Tomorrow I’ll try to write the rest of the explanatory text so I have a few days to let it mellow before sending it off to the printer.

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Being connected is liberating (duh)

We’re just back from a quick road trip, a micro-vacation to explore nearby Cleveland. We visited the Rock & Roll Hall of Fame and Museum and the Great Lakes Science Center. I’ll write a little more about those later, but I wanted to capture my initial impressions of my first connected road trip, by which I mean one with an iPhone and a data plan.

In a word, it was liberating. Not having to nail down all of our plans in advance, we could be more flexible and adapt to the energy level of the kids. This is another way of saying we could be ourselves and pretty much make things up as we went along.

Having turn-by-turn navigation was huge, and Google Maps was outstanding. I used Apple’s Maps to start, but after giving Google Maps a try, I stayed with it. My stress level was noticeably lower knowing I didn’t have to figure out where to turn to get back to the highway from the museums. There were a few little, tricky turns that I never would’ve found without the help.

I quickly found a great little pocket of restaurants to choose from near the hotel, including a Thai place and a Lebanese cafe, where we ended up eating.

Of course, none of this is impossible without a connected phone. I know I’m late to this party, too, having settled for iPods and iPads until I could get an iPhone on my terms, not those of a carrier. Knowing we would be traveling this month, I paid for a month of data, and will likely return to a minimal plan next month.

Interesting to note that, even when using it as the impulse struck, I only consumed about 18 MB for the whole trip. I could probably get by on the 500 MB data plan and still get a lot of value when we travel.

Pages for a poster

Yesterday I wrote briefly about getting to work on a poster to present at a conference in a few weeks. After working on it for a bit, I’ve decided to switch to Pages from OmniGraffle.

While OmniGraffle is certainly more than capable for the task, I’m finding it almost too flexible. In the same way that I’m drawn to outliners for writing, I’m drawn to Pages for a little more structure in the layout process. I could probably figure out how to make OmniGraffle give me that structure, it’s already done for me in Pages.

I created a new document in Word Processing layout, which may not seem intuitive for layout work, but it keeps me from having to fiddle with making all the text boxes individually. After creating a new file, I changed the page size to my poster dimensions – 30 inches wide and 40 inches tall in this case. Then I put in the title and author details and inserted a layout break. After the break, I set the layout to 3 columns and let the app automatically size them.

Harpoon Craft Cider

harpoonI’m not a big drinker, but somedays just seem to call for a little something more than water or iced tea. Even though I’ve been a home brewer for many years, lately I’ve found that beer makes me sluggish and sleepy more than anything, so I’ve been sampling as many ciders as I can find this summer.Arsenal 2017 movie

Tonight I picked up a few singles at one of our great local craft beer shops, and one of them was Harpoon Craft Cider. It’s amazing the difference in complexity between this and, say, the Michelob hard cider I bought before it. It’s like the difference between eating an apple and an apple-flavored Jolly Rancher! It’s a very well-balanced, light, crisp drink with a complex collection of flavors. The 4.8% alcohol is low enough that I can do other things while drinking it (like write this), yet still feel a little more relaxed.

The only slight downside is that I’m getting a little hint of a cedar or wood note. It’s not enough to make me not want to drink it, but it’s there nonetheless. I’ll buy it again!

Poster prep for ASPB 2013

I started working on our poster for ASPB 2013 today, revising my student’s previous version to add new data and generally smooth out the rough patches. I’m using OmniGraffle to do the layout, since I don’t have to share it with anybody else during the editing. It’s a bit of a luxury not to have to use PowerPoint for the layout, which is the least common denominator that I’m usually stuck with for this job.

Rather than simply transfer our figures on the old version into the new one, I’m going to take this opportunity to make publication-quality figures with my tool of choice, DataGraph. This is also a great chance to think about the data we have and what we still need in order to finish this project.

I’m trying to use a grid-based layout for the poster to impose some structure behind the scenes. The poster’s 40 in wide, and I’m working on 4 × 9.5 in columns at the moment. Not sure I’ll stay with this, but it’s a start. I’ll have to see how well the various graphs fit this grid before I commit to it, and I’m still working on those.

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Scalia’s belief in DNA

Justice Scalia, in his concurrence in the Myriad Genetics patent case:

I join the judgment of the Court, and all of its opinion except Part I–A and some portions of the rest of the opinion going into fine details of molecular biology. I am unable to affirm those details on my own knowledge or even my own belief.

What does this statement mean? The article from which I quoted him (linked above) argues that Scalia here is making a proud statement about his ignorance of the details of molecular biology, and that this scientific illiteracy is a badge of honor among much of society. I’m not so sure, especially given:

Typically, Justice Scalia does not qualify the factual portions of opinions he joins, even where they involve science.

I don’t have any good thoughts on what he has in mind with this qualification, but I find it disturbing. At the same time, as someone who teaches the fundamental concepts at play in this case to students of the liberal arts, I hope none of my students make such a claim when they become Supreme Court Justices.

Writing about science for the public

Some good bits of advice for writing about science for the public, including this one:

Readers can be very clever, but it is not their job to know all of the words that you and the twelve people you call colleagues made up.

I particularly like the focus on telling a people-centered story. This is so far from the comfort zone for most researchers, but I agree that it’s essential to effectively connecting.

Answers or exploration

New Lemurs logoI’ve read more and more in recent years about ‘gamifying’ education, and I have to admit, I never got it. This helps to put it in a little more context:

If what you want is an answer and not an exploration then I don’t recommend pretending you’re looking for an exploration. Students are very attuned to bullshit.

Using gaming to engage students and teach certain skills like exploration and problem-solving makes some sense to me.

It also reminds me of an episode of the Debug podcast I listened to recently, with software developer Mike Lee. His current company made a chemistry game for iOS based on actual chemical reaction modeling. Lee tells the story of creating the game in the interview, and how the lack of access to real chemistry sets for kids these days played a small roll in the idea, but rather than trying to replicate mixing chemicals on the iPad, they approached it from the standpoint of letting the technology do what it’s good at. Taking that approach, it seems like there are so many opportunities to create games that teach, it’d hard to know what to work on next.