What is a Bridgehead Carbon anyway?

It's the start of a new school year and I am going to try to post a little more regularly.  Since it has been a while since I posted on a regular basis, I thought it would be a good idea to re-introduce this blog.

What is a Bridgehead Carbon anyway?  I teach undergraduate chemistry and my main area of interest is Organic Chemistry.  I chose the name "Bridgehead Carbons" partly because I have always liked the look of bicyclic compounds like norbornane.  You can think of Norbornane as being a cyclohexane (in pink) with a CH2 unit (in black)that acts as a bridge connecting the top and the bottom of the pink ring.  The carbons that connect the "main ring" to the "bridge" are the Bridgehead Carbons.

Another reason for choosing this name is that Bridgehead Carbons serve to connect different rings within the same molecule, and I intend to write about a variety of topics that I none the less feel are connected to my experience with chemistry and teaching.

So, what is this blog all about?  Stuff that interests me as a chemistry teacher, especially organic and bio-organic chemistry, cheminformatics, things that might be helpful to college students in general, and anything else that strikes my fancy.

End of the Year Writing Advice

It is the end of the school year and our seniors will be turning in their senior research papers soon.  I think that scientific writing in particular can be a big challenge, especially when writing about your own research.  When you work on a project for most of a year you become emotionally invested in it, and you loose sight of its complexity.  But in sharing your results with others, whether as a paper or an oral presentation, it is easy to assume that everyone knows what you know.  And when discussing complex ideas, you can try to say too much at a time.

The original list has seven rules, but I am only quoting the first three.  If you are a writer of any sort, go read the original post with all seven rules.

VS Naipaul’s Rules for Beginners 

1. Do not write long sentences. A sentence should not have more than ten or twelve words. 

2. Each sentence should make a clear statement. It should add to the statement that went before. A good paragraph is a series of clear, linked statements. 

3. Do not use big words. If your computer tells you that your average word is more than five letters long, there is something wrong. The use of small words compels you to think about what you are writing. Even difficult ideas can be broken down into small words.

The point is to use good judgement.  Use big words when they are necessary, not just to impress your reader.  Strive for short, direct and clear.  If the result is too simple, you can always revise.  But if your first draft is full of long, convoluted sentences it can be hard to make it concise.

Sometimes you don't really understand some of the details yourself.  Really good writing can help you to better understand the topic yourself.  It forces you to choose your words carefully and think about the meaning.  

VS Naipaul’s Advice To Writers - The India Uncut Blog - India Uncut via BoingBoing

Tabla Periodica de los Elementos

Ever wondered what the Periodic Table would look like in a language other than English? The Chemistry site at About.com has one in Spanish. Look for the link to the PDF version underneath if you want a nice copy to print. It even includes the newly named element 112 Copernicio (Cp)

Tabla Periodica de los Elementos

Science Careers Booklet from AAAS

The Association for the Advancement of Science (AAAS), publishers of Science magazine, have put together a booklet of advice for people planning on a career in science.  There are chapters on graduate school, skills for scientists, resumes and networking, non-traditional careers, diversity issues and others.

The articles were originally written for their careers web site and have been collected into an 88-page booklet.  You can see the original articles, individual chapters, or download the whole booklet as a PDF file.  And it's FREE.

Career Basics Booklet - Biotech, Pharmaceutical, Faculty, Postdoc jobs on Science Careers

Monastic Musings: How can I be failing? - Unskilled and Unaware of It

A while back I found this article over at Researchblogging.com

Monastic Musings: How can I be failing? - Unskilled and Unaware of It In this post, Edith osb writes:

I noticed a surprising phenomenon last semester. Several first-year college students were getting consistently low scores on chapter quizzes - and they did not seem the least bit bothered or concerned about it. They were similarly unperturbed about scores below 60% on the first exam. When they received their mid-semester grade report, though, two of them came to see me, astounded to get such low grades. Their surprise was, of course, surprising to me: how could they possibly think that they were doing well when their quiz and exam scores were in the 50% to 60% range? They claimed that they were unaware that they were doing so poorly, and were somewhat angry that I had not "told them sooner."

A few years ago I had a student come to see me after final grades had been turned in.  The student had failed the class and was in tears, "Is there anything I can do to improve my grade?"  I was stunned, and explained that it was too late. Final Exams were the week before and the semester was over.  I gave 4 midterm exams and a Final Exam, this student had failed every one of them.  How could you not realize that you were failing the class?  Each of those exams was a clue that the student needed to get help.

I have always felt that college students should be treated like responsible adults.  It is their job to pay attention to their grades and get help when they need it. But reading Edith's post, and the article that inspired it, I am reminded of how easy it is to fool yourself.  I was not a particularly good student as an undergrad, and I often reassured myself that I would do better on the next exam - this did not tend to happen.  Realizing that you need help is difficult, and asking for it can be even harder still.

But there may be something else at work in addition to rationalizing and avoiding things that are difficult or uncomfortable.  In "Unskilled and Unaware of It: How Difficulties in Recognizing One's Own Incompetence Lead to Inflated Self-Assessments," Kruger and Dunning are interested in how people judge their own abilities. They looked at four different studies where the subject was given a task to complete, and then asked to predict how well they did.  

All of the subjects in all four studies tended to rate their own performance as above average! (How can everyone be above average?)  The subjects with the lowest scores thought that they had done much better that they really did.  The subjects with the best scores still rated themselves as above average, but generally below their actual scores. From this, the authors conclude:

We propose that those with limited knowledge in a

domain suffer a dual burden: Not only do they reach mistaken

conclusions and make regrettable errors, but their incompetence

robs them of the ability to realize it.

In the case of chemistry students, for example, this means that the students who don't know what they are doing also don't realize that they don't know what they are doing.  It is almost impossibe to correct your mistakes if you don't realize that you are making mistakes in the first place.

Consider American Idol.  If you have ever seen any of the audition shows you can see this in action.  The really awful contestants usually have no idea how bad they are, not a clue.  And they don't understand why the judges don't give them a ticket to Hollywood.  In contrast, a lot of the really good singers are much better at judging themselves reliably.  They know they sing well, but don't tend to over-estimate their ability.  They are often much better singers than they think they are, and seem a little surprised when the judges like their performance enough for a ticket to the next round in Hollywood.

Back to Edith's post.  She and some of the commenters suggest that some High School students - for a number of reasons - may not get trustworthy feedback on their academic skills, and because of that are not able to tell good work from bad.  They haven't learned to tell the difference. Or don't realize that it matters.

I have tended to downplay letter grades during the semester  - many things affect a student's final grade and one bad exam score can be offset by the remaining exams, quizzes and laboratory grades. I can't really predict a student's grade until everything has been graded.  I have also worked from the assumption that the student can tell that a exam grade below 70% means a D, which is close to getting an E (my school doesn't give F's, maybe the letter E is a little less judgemental) and realize that unless they do something about it they will be disappointed with their final grade. 

I think I may change that practice and start putting letter grades on exams and quizzes to help the low performing students learn to recognize unambiguously that they are not doing as well as they would like. I highly recommend reading both Edith's post (and the comments) as well as the original paper itself.

Blogging for Extra Credit

I don't normally give extra credit assignments in my classes.  I figure that rather than doing "extra" work, the class should focus on mastering the material we work on every day.  However, we have had a challenging semester and I wanted to give the class something fun to do that might help their morale (and grade)  and encourage them to read about science outside of class.  I asked them to write to me about something interesting that they had read about science, something from my blog or any thing else that strikes their fancy.  

It's always fun to see what students find interesting when they are left to choose the topic themselves.  Here is what I learned from my class:

Mikaela wrote:
Although my intentions were to look at one article and write about it, I seem to have got lost in the wonderful world of blogging and spent a little too much time on the day before exams surfing the web. Of the several I looked at, I enjoyed three in particular. First, I read about the study on caffeine versus napping. This was interesting to me because I am a firm believe of napping! I've never really been a caffeine person; I very rarely drink pop and maybe have a cup of coffee once a month. Caffeine does not really make me feel energized or more alert so I tend to just stay away from it. Napping, on the other hand, is probably the best part of my day. Although I don't nap as much as I'd like to, I always feel completely recharged and very alert once I wake up. I often nap before tests or quizzes instead of stressing and cramming minutes before because I do best when I am relaxed. After reading, I was curious to see the whole article and different experiments they did. 

The second article I read was on the glowing mushrooms. This was interesting to me because I like hearing about abnormal things that occur naturally. I love that nature has so many undiscovered features and that it encourages us to never stop exploring. 

The third article I liked was five reasons you should pick up a pencil and draw in "Getting Things Done in Academia." I have always found drawing as a release from all my other academics. I took four years in high school and it was my favorite part of the day because I got to unwind. I like the idea of linking art with sciences (particularly anatomy) because I think once you try sketching something, you look at the object your drawing in a different way than you ever thought you would. Noticing the small details makes the animal come alive, and that much more beautiful.

From Jenna:
I read through your blog and found a few interesting things. The first thing that stood out was on Mutagen, how drugs can be very effective, yet they can also have bad side effects. It is interesting that they can predict the toxicity of the compound before making it. Since I have started college, I have had many people ask me what courses I am taking. When they hear me say chemistry, they crinkle their noses and say "Yuck! I don't understand why anyone needs to take that! What good is that going to do to help you in the real world?" That's just it, many of them do not understand, or at least do not think about it. The first thing that comes to my mind is, "How do they think aspirin and other pain relievers came to work? Along with their cholesterol meds?" Since I began taking chemistry, especially organic, I have developed a deeper understanding of how chemicals work, and I think it is important to realize that chemists really do make an important impact on the world. Now, back to your blog, I agree with what you said about media portrayal. It seems every time you watch t.v. you see commercials for a new drug and they spend over half the commercial telling you all these horrible side effects it has. It's no wonder why so many people are afraid of chemistry. The media mostly portrays things like this involving chemistry, I think they don't portray the good things about it mostly because they are not well enough educated in chemistry to understand-most of them are biologists.

I also laughed about the high fructose corn syrup. Also, the brightly colored fruits and dark leafy green being defined as a fat. Even I know that's not true! I probably have my mother to thank for that!

I found an interesting article about Lions, Tigers, and DNA.  A scientist started studying feline leukemia in the 70's and found diseases. I find this interesting since I have worked for a few vets for the past 3 1/2 years and have done multiple feline leukemia tests on cats. These tests have been made possible because of scientists who have spent years studying it. I also find DNA and reproductive traits very interesting in animals. I hope to study animal genetics and reproduction more in depth when I go to vet school. The scientist also studied feline HIV to fine a gene that might help create immunization for people. This is another example of how scientists and veterinarians can to reasearch on animals to help understand and find treatments for people.  He also found genetic mishaps during migrations of felines, and he published his research in Science.

Amanda:
I found an interesting article about finding a new earth.  They have no real evidence but the star that they did find is one third of the mass of our sun, and when they first found the star there was a planet circling it and pulling the star at the speed of a jet plane.  Then they saw another planet rotating and it was pulling the star at the speed of a race car. After the most recent observations they found a third planet circling the star much more slowly, it rotated at the speed that a man could run!  I thought it was cool because they went on to say that the planet had a rocky content similar to ours. They also said that it is 15 million light years away, so the thought of a new planet is still far away, but really cool!  I think that we should try to keep our planet and restore it but the thought of other life forms is exciting.

Carla:
I was searching online for articles about Organic Chemistry and came across a very interesting one that might be of a little interest or just a fun fact to learn about for you.

As the article says, "A discovery by a NASA scientist of sugar and several related organic compounds in two carbonaceous meteorites provides the first evidence that another fundamental building block of life on Earth may have come from outer space."

How interesting is that, that a fundamental building block of our life could come from outer space! I guess in previous research, researchers found that meteorites have organic compounds found on earth, like amino acids and carboxylic acids. This information is helping researchers understand that there could have been organic materials on earth before life. If you want to read more about it, the website is http://www.sciencedaily.com/releases/2001/12/011221082306.htm

Brad:
I thought you all might like these topics… some relate strongly to organic chemistry and its affects and some deal with chemistry and physics and some are just plain interesting facts I thought you all might like to look into….so here is a list with links…

1. Is Carbon nanotubing… I first read about this material on an article that was titled “space Elevator” why it was call that is that the unique structure of this carbon sphere was a fraction the weight of steel and was around 10x the strength of steel, which made it a good candidate. http://www.personal.rdg.ac.uk/~scsharip/tubes.htm 

2. This topic is a little hard to find…. Saw this on the history channel which was kind of cool how Hannibal in around 220 b.c. conquered Rome by attacking them through the mountain range the Alps. What made this so unique was Hannibal was said to be crazy to attempt this by taking 10,000 people and horses and war elephants on this trial over the mountain. He had no problem scaling the mountain where he ran into trouble was the descent. He ran into steep limestone rock faces they could go down and they couldn’t turn around either. As they sat there his chemist as you might call them found out if you heat limestone up and pour in their day was wine vinegar it would react and produce CO2 and H2O. Once cooled the rock became very brittle and they were able to make a zig zag path down the mountain face. As for a link with this I have looked for the story and havent found one you may be able to look up on history.com and check for times the program maybe showing.

3. This topic is just rather interesting that relates to chemistry and slighty organic chemistry if you look up the term Browns Gas you will find an interesting topic. I heard about this at work they explained it to me in the simplest way as they thought it heated up any given material to the temperature at which it melts and does just that… I guess these links will explain it in more or more accurate detail. http://www.eagle-research.com/browngas/whatisbg/whatis.html http://en.wikipedia.org/wiki/Oxyhydrogen 

4. This topic is for anyone who wants to do some good with their computer and also get a viewing of a construction of a large carbon molecule from a simple core model. This is a program you can download called Folding@Home what it does is use your computer to fold organic molecules in an attempt to develop a molecule that can help them fight cancer. If you want to do this simply google the program name and go from there. It is a good way to view large organic molecules and how organized they are, I have had this program for a year I still run it to this day.

5. Well its not a big secret that there are more bio majors than chem majors so here is something interesting for bio majors. I don’t know if this relates to chem, but people tell me they have never heard this before so here ya go. There was these two Russians playing in a chess tournament Nikolai Titov and Vladimir Dobrynin and all of a sudden while Titov was in deep concentration on the board he screamed in pain and grabbed his temples and his head blew up like a fire cracker. Now I know you may think im pulling your chain but it’s a rare condition call HCE Hyper-Cerebral Electrosis. Now not getting into to great detail the gist of the story is not to think to hard or your head may blow up…Literally! …. If you want to read the article let me know and I will bring the book in.

Need a Quick Pick Me Up? Take a Nap.

The New York Times has a short article about a study that compared caffeine with taking a short nap before doing mental and physical skills.  As it turns out, the people who took caffeine felt more awake, but they didn't score any better.  In fact the caffeine group performed worse than nappers on all three types of task that were studied:  motor skill, perceptual task, and verbal task.

I really like my coffee, but it is no substitute for getting enough sleep, and even a short nap in the afternoon will do more good for you than just caffeine.

The research paper itself is available online.  You can read the abstract for free, but to read the full paper you need to be a subscriber, or you can pay for it for $31.50.

Vital Signs - Regimens - For the Best Pick-Me-Up, Lie Down - NYTimes.com

Hat tip: Lifehacker.com

Advice for Students

Have you ever had a hard time keeping up with all the things you need to do as a student?  Take a look at the Alpha Student web site.  It is run by a couple of college students in England.  The articles are listed in catagories: Academic, Career, Financial, Fun, Personal, Practical and Social.

Most of the articles are written by Ali Hale who is in a masters program in creative writing.  Take a look at this interview with Ali.  It makes me tired just reading about all of the different things she is doing while in graduate school - she writes for a bunch of blogs in addition to Alpha Student, and she did all of the coding for Alpha Student (html, css, and php).  

Ask Questions - Stepcase Lifehack

Ask Questions - Stepcase Lifehack

When I was an undergrad I tutored Organic Chemistry.  One of the students I tutored was a biology major and a friend - Kathy was also in the karate club,  but that's another story.  She was a challenging person for me to tutor - because she asked questions.  Specifically - "Why does that reaction happen?" and "How do you know that is the product?" and other inconvenient questions.  I could tell her the answers to her homework problems, but answering these questions took effort.

I'm grateful to her - she made me think.  And trying to answer her questions forced me to understand them myself.  Asking questions and trying to answer them is an important step in learning new things. Even asking yourself questions and trying to answer them yourself.  Don't be complacent!  Be curious!  Ask questions!

Take Time to Unplug Occasionally

I know I spend way too much time surfing the internet. It is a good idea to go unplugged every now and then in order to really get things done. I was reminded of this when I saw 10 Ways to Ungeek for Productivity Just the other day I took one of my classes to the library, so I could really relate to #5:

5. Do Research at the library

Despite what I’d like to think, Google can’t find me every detail on every topic. Depending on what I’m researching, I often go to the public library. Many libraries maintain subscriptions to databases that cost quite a bit to access, but they also have plenty of offline information. I make a habit of chatting to one of the librarians about what I’m working on. They can often point me to references that I might not have thought of or show me connections between my topic and another that I never would have found searching for keywords on the web.

And there are times when a change of scenery can do wonders for your attitude - get out of your room / office and go somewhere else to work. Besides, I like books.  

Finally an Unplugged interlude with Eric Clapton from back when MTV had music.

See if you can spot this one.

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.

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 Lifehack.org. 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.