Sunday, September 28, 2008

Going to School for Fun

Wouldn't it be cool to go to school just for fun?  To take classes because you were interested in the subject, without having to worry about grades or money?  Turns out that Flea, the bassist for the Red Hot Chili Peppers is doing just that - at 45 he is a freshman music major at USC.  

Yesterday I heard an interview with Flea on NPR's All Things Considered.  Check it out.  As a chemist, and occasional musician, I especially liked this quote:

"Music is made up out of these building blocks," he says. "Studying how these blocks go together and what they consist of and the math of how it works — it's all the same stuff; it's just different aesthetics that we're talking about."

That could apply to almost any field.

I have to say that I'm envious.  As a teacher myself I do have a lot of freedom, as well as an obligation, to keep learning new stuff.  But I don't have the time to really immerse myself in quite the same way.  It would be fun to be a student again.

Thursday, September 25, 2008

James Bond Molecule bag

I saw this cool bag over at  I had to get a larger image to actually see what the picture is.  It shows the gun barrel shot seen at the start of the James Bond movies, with a molecule of some sort.  Being a geek, I had to figure out just what the molecule is.

Over at I was able to draw the structure in the editor and do a search.  The compound is called Sulforhodamine 101 acid chloride.  eMolecules provides a little info on the compound as well as links to chemical suppliers and listings in PubChem.

I just want to know what it's used for, so a quick search on Wikipedia turns up two listings:  one for Sulforhodamine 101 and another for Texas Red.  These are related compounds that are primarily used as biological dyes.  They are highly colored (red, in case you couldn't guess) because of the large amount of conjugation, and as it turns out they are also highly fluorescent. 

The difference between Texas Red (the acid chloride) and just plain sulforhodamine is the acid chloride has a chlorine in place of one of the OH groups.  This makes it very reactive with proteins especially - an NH2 on the protein acts as a nucleophile to replace the chlorine - leaving the protein with a bright red label attached to it.  Texas Red is especially convenient in that the acid chloride will also react with water, and the resulting compound is water soluble and can be rinsed away.  This means that only the dye molecules that are attached to the protein remain - excess dye can be washed away.  Other methods of labeling proteins aren't always so helpful - any excess dye may remain and obscure what you are interested in seeing.

Wednesday, September 24, 2008

Advice for Students

Most college students are so focused on the next assignment (or athletic event, or party) that planning ahead for post-graduation doesn't get much attention. Ironically, career planning can be rather like studying - you make it a habit to study every day and the exam will usually go well. If you procrastinate and cram at the last minute you will be stressed-out, not as prepared as you should be, and you probably will be disappointed in the results.

For some ideas to help you plan ahead, take a look at this post at I especially like #6 "Pay Attention!" Most things you see on self-help sites are really common-sense. But if you don't do anything about it, having common sense doesn't help much.

Thursday, September 18, 2008

Bee Vomit and Spider Silk

I rather like Bee Vomit, although I don't think I would put it on my peanut butter - I've always been a bit of a purist when it comes to peanut butter sandwiches. Spider silk is pretty cool too.

Wednesday, September 17, 2008

Sunday, September 7, 2008

Start of School

We're two weeks into the semester now and things are starting to settle into place again.  With the start of a new year there have been a bunch of changes, and of course not everything went smoothly.

First off, I have decided to try something new with my Organic Chemistry class. Lately I have been concerned that despite my best efforts, my students were not getting the most out of my lectures or the readings in the text. Using some student activities during lecture is something I have tried in the past, but I always drifted back to straight lecture. Over the summer I got two presents in my mail box:

  1. not one, but two copies of Organic Chemistry: A Guided Inquiry, which uses a POGIL approach

  2. a booklet on Using Pogil in the Classroom and Other Research Developments from last November's meeting of the Michigan College Chemistry Teachers Association

This seemed like too good an opportunity to miss. As a result, I am replacing my standard lecture format with POGIL. POGIL stands for Process-Oriented Guided Inquiry Learning and involves the students working in groups during class time, with me monitoring and guiding the groups when they have difficulties. The text is really more of a workbook which the students use during class that guides them through the process of learning each lesson. They need to have the book with them every day in class.

It is still a little early for me to tell, but the students seem to be adjusting – some better than others, but that is only to be expected. Of course, the students turned out to be the least of my problems in adopting POGIL. The second edition of Organic Chemistry: A Guided Inquiry, the POGIL text I am using, came out over the summer. When I went to our bookstore manager in July to ask about switching texts he told me there wouldn't be a problem and we should have the books before class started. Ha!

As it turns out, the publisher was out of stock and didn't expect more until Sept 5 – two weeks into the semester. This is at minimum a nuisance, but if the students NEED to have the book with them in class every day to do the lessons it makes it difficult to stick to a schedule. My bookstore manager was very helpful, he was able to get the first few sections of the book copied for me by the first day of class – so we were covered with about two weeks worth of class activities. The author, Andrei Straumanis, has a pretty active listserve on using his book and the POGIL system. He got permission to post pdf's of the first few weeks worth of the book on his web site.

Friday the bookstore called to say the books were in. Hurray!