Sunday, October 28, 2012

Balloon representations of VSEPR shapes

It seems to be very hard for students to initially picture the VSEPR shapes of molecules. They draw the Lewis dot structures and then get really hung up on trying to visualize how the Lewis doc structures correlate to the VSEPR shapes.

Here is my visual aid. BALLOONS!
It really is the best way to picture it- it is better than a model kit and better than trying to draw it three-dimensionally.
The two green balloons represent a linear molecule spread at 180 degrees. Typically without steric hindrance any two atom molecule will be a straight line like these two balloons.
The next two drawings represent the most mistaken structures. The trigonal planar (three balloons) and the tetrahedral (four balloons) are actually very, very different shapes. The trig planar is two-dimensional (flat) while the tetrahedral is three-dimensional. This is tricky because if one of the balloons in the tetrahedral is a lone pair of electrons (empty cloud without an atom) the structure becomes a trigonal pyramid. This is NOT the same thing as a trigonal planar molecule. It is still three-dimensional- it just has an empty space where one of the clouds previously had an atom.

I don't include the trigonal bipyramid and the octahedral in my class but those two structures are included just to get a preview of what people study at the next level of chemistry.

Build these structures to fully understand VSEPR! Don't mix up your trigonal pyramid with your trigonal planar molecules!

Thursday, October 25, 2012

Spiderman, Regenerative medicine, the 2012 Nobel Prize and the future....

Dr. Curtis Connors from Spider-Man

The most recently released version of Spiderman shows a mad scientist obsessed with his own ability to transform himself into a lizard. It all starts as part of a science experiment gone wrong- he's using an injection from his lab to try to grow back an arm that has been chopped off. In the process of just trying to regrow his arm, he ends up transforming himself into a completely different creature. This is just one example of synthetic biology that shows up in our lives. In this case it is purely fictional in nature. It may not always be that way.

This year the 2012 Nobel Prize for medicine went to two men (Sir John Gurdon and Shinya Yamanaka) for a discovery about stem cells that could bring this surreal, onscreen entertainment into reality. Both men contributed to the effort to manipulate stem cells in the body. Certain stem cells are blanks in that they don't start out with the same function for which they end up. If researchers manipulate them correctly, it is possible they could clone an entire human being. It also opens the door for the science fiction lizard of Spiderman to become a reality- this technology would allow cells of any variety (or organ) to be grown from a small sample of other cells.

In an essay for the Wall Street Journal last weekend, George M Church and Ed Regis write about larger applications of this technology in synthetic biology. Regenerative medicine just scratches the surface of what we are able to manipulate with genes.

"It is now routine to genetically reprogram microbes to make plastics, biofuels, vaccines and antibiotics. They have been engineered to detect arsenic levels in drinking water, destroy cancer cells and store digital data in DNA, making bacteria into biological flash drives."

And apparently resurrecting life from the dead is also a claim of synthetic biology:

"As for resurrecting extinct animals, this has already been done. In 2003, in Spain, a tree fell on a 13-year-old female goat named Celia, killing her. She was the last living Pyrenean ibex, a subspecies of wild mountain goat, which thereupon became extinct. A few years earlier, fortunately, a Spanish biologist had taken skin scrapings from Celia's ears and stored them in liquid nitrogen in order to preserve the ibex's genetic line. He and his team removed the nucleus from one of these ear cells, transferred it into an egg cell of a domestic goat and implanted it into the uterus of a surrogate mother, who gave birth to a live Pyrenean ibex."

Another potential application is to kill the replication method of viruses and render them ineffective.

"If you change the genetic code of the host cell, as well as that of the cellular machinery that reads and expresses the viral genome, then the virus could no longer replicate."

Regenerative medicine and synthetic biology seem to pervade the news these days with surprising abundance. Is this a sign that the field is on the verge of real discovery or is this just more hype on a trendy path of science fiction? Only time will tell.

Sunday, October 21, 2012

#ChemCoach: Adventures in Working.....

In honor of National Chemistry Week I am participating in #ChemCoach hosted by See Arr Oh of Just Like Cooking blog. I am supposed to write a  summary about my current job.

Your current job.

What you do in a standard "work day."

What kind of schooling / training / experience helped you get there?

How does chemistry inform your work?

Finally, a unique, interesting, or funny anecdote about your career*

I am, by title, an Associate Faculty member of various junior colleges in southern California. This means that I teach chemistry classes at various schools based on the needs of the school at any given time. This also means that it is very easy for me to come in and out of the field on a semester-by-semester basis. In June 2011 my first child was born and I decided not to take any classes for the fall 2011/spring 2012 year. Then, in fall of 2012 I committed to teaching one class.

On the days that I teach I get up at 5 am to drive up to Orange County. Initially, the drive up there was horrifying to me- I had never done it regularly aside from a yearly trip up to Disneyland or Universal Studios. However, when I leave my house at 6 am there is absolutely no traffic. None whatsoever. I can relax in my car, pop in a CD and have an enjoyable drive up north. (On the flip end, I get off work at around 11 am and drive home. The traffic is very minimal at this time of day.)

Usually I arrive at work about forty-five minutes early. This gives me enough time to take care of loose ends: visit someone on campus for business, prepare my white board for class, boot up my computer,  make sure I have a waste container and all proper equipment if it is a lab day. Then, class starts. Students arrive by 8 am and sign my sign-in sheet. They turn in their labs from the previous week and we settle in for the daily "lecture." (For lack of a better term it is still called a lecture- I wish it wasn't.)

We take a break at 9:30 am or so and by the end of class we do the "clicker" slides. These are slides that allow the students to select an a,b,c,d answer for a question pertaining to the lecture. It gives students a chance to participate and it gives me feedback about what they understood and what they missed from the  lesson.

Then, at around 11 am we finish class and everybody goes home. My duties outside class include grading labs/quizzes/exams, answering student questions via email, maintaining my blackboard site and providing keys for all quizzes, tests and other assignments. (All of these are posted on my blackboard site.)

My job requires at least a master's degree in chemistry. Many people with a PhD also do this work but the PhD is not required.

Something unique about my career? I was hired as a chemistry instructor at a junior college as the result of a flute performance I did at a church in La Mesa. It was the most unusual way I've ever been hired in my life. An usher approached me at the end of the performance and asked me about my day job. He was a professor/instructor at a local college. The rest is history.

Tuesday, October 16, 2012

"You’re really going to make my son spend a whole year in a subject he will never use so that he can prepare to suffer at a boring job some day? "

The title of this article was copied from a post on a blog of The Washington Post. This particular statement provoked some strong feelings I've developed about basic science education.

We must require basic science literacy of our K-12 students. If we do not, we are not preparing our students to think critically, make informed decisions and harvest all of the pleasure and reward of an adult life. Learning science is about so much more than preparing for a specific job after college or vocational school. It is about seeing how science applies to everyday life and using that knowledge to improve everyday life.

Does anybody know when they are a sophomore in high school what their major will be in college? Maybe a few of us do, but most of us don't. Most American high schools are already deficient in preparing high school students to major in science in college (let alone chemistry which is more difficult than some other science majors).  How can we expect our students to choose a science major at all if we don't require (at least) an exposure to it at the high school level?

A response to this question might be the following: "Shouldn't the kids be able to choose what science they take at the high school level?" My answer is no. An exposure to science includes the building blocks of all types of science; at this point most fields of science are fairly interdependent. It requires a basic understanding of one field to gain a basic understanding of another field. They must have one year of chemistry, one year of physics, one year of biology and a year of freshman science (or something similar). If they take just this much science, it is my opinion that they are not really well enough prepared to major in science at college. To be successful at an undergraduate level in science (especially chemistry) you need to take two years of chemistry, two years of physics, two years of biology plus any freshman science requirement the schools provide. (Some schools have a freshman science class that is a hybrid of science types.)

Based on my assessment of what an adequately prepared freshman would have to take to be prepared for college, one year of high school chemistry is nothing. Nothing at all. It is a bare-bones exposure with a minimum of information. And here is what that year of chemistry will sow in a child's mind:

1. A knowledge of basic elements: what is dangerous, what is benign, what chemical under their kitchen sink must absolutely be removed when babies are born. (namely sodium hypochlorite)

2. An appreciation of where we've come since the advent of quantum mechanics. All of the gadgets, electronic devices and common household items we all take for granted are a result of the quantum mechanics revolution. The digital world has changed the way we function in an absolute way.

3.  A basic understanding of energy: What are energy sources and how does chemistry influence energy sources? How do humans interfere with this process? How is nuclear energy important and what is the basic chemistry of nuclear energy. With the price of gas rising, I'm sure we all agree that international energy resources are critical to the functioning of our nation. Everybody should understand these resources from a chemical perspective.

4. A fundamental understanding of how chemicals affect the human body. Our body is made naturally of chemicals. Sodium/potassium channels, water (H2O) and many other chemicals allow basic processes to allow us to live and breathe each day. How do the chemicals we add from outside our bodies interact with natural human chemicals on a daily basis?  My own grandmother never took chemistry and it was very obvious when she spoke about the drugs she was taking. She had no fundamental understanding of chemical processes in the human body.

On top of all of this- is it really fair to pigeonhole a child into a nonscientific career at such an early age? This is what you are doing by default if you do not require them to take chemistry. Science knowledge builds like a pyramid. Without basic chemistry, a child could never take biology or any of the other classes that apply basic chemistry. (This is why people like me never suffer unemployment- since everybody must take basic chemistry for their major there is never a shortage of basic chemistry courses to teach.)

Kids need science. Our world needs science. Way beyond any career decisions we make later in life - we all need to attain a basic level of science literacy.

Yes, all high school kids should be required to take one year of chemistry. At the very least.

Friday, October 05, 2012

Frustration over the Empirical Formula Lab

Why is it that every year we do this experiment and every year people get ratios that don't make sense? I thought that if you put the lid on your crucible right after the magnesium sparked (and starts to smoke) that you wouldn't lose material. This would result in accurate calculations for the ratio of magnesium to oxygen in magnesium oxide.

Right? Wrong. Every year people get the wrong ratio and I can't figure out why. Is it miscalibrated balances?

I have no idea. I wish I knew.