Saturday, March 14, 2009

Molecular Frameworks in Wired

The latest issue of Wired magazine has a chart of the top 30 molecular shapes in the Chemical Abstracts Service database of more than 24 million compounds.  Their definition of shape is based on rings and linkers which connect the rings, nothing else is considered: not the side chains attached to the rings or their connectors, presence of multiple bonds, or the elements involved.

As they point out many of the compounds listed are naturally occuring, or synthesized with natural compounds as the starting point or inspiration.  Not surprisingly, the most common shape they identify is a hexagon and the second most common is the pentagon. The preferred bond angles for most organic compounds are around either 109 degrees or 120 degrees. Four- and three-membered rings (squares and triangles) aren't that common in nature - they do not appear in any of the top 30 shapes.  These small rings have much smaller bond angles, and feel a lot of strain when forced to have such compressed bond angles.  5- and 6-membered rings have effectively zero ring strain and are very common in nature.  Larger rings can also have ring strain issues.

About half of the top 30 shapes include a pentagon, but there is one or more hexagons in every one of the top 30 shapes except for shape #2 which is a simple pentagon.

Wired:  Molecular Frameworks, the Building Blocks of All Life

Watch: Sita Sings the Blues

The Ramayana is a Hindu epic that tells the story of Rama, a prince from the city of Ayodhya.  Sita Sings the Blues is a wonderful re-telling of the Ramayana told from the perspective of Rama's wife Sita.  It isn't a happy story: Sita goes into exile with Rama, she is kidnapped and rescued and her faithfulness questioned more than once.  

Nina Paley has put together a marvelous presentation of this story using several different styles of animation and music.  The story is interwoven with commentary by three shadow puppets as well as scenes from Ms. Paley's own life.  An integral part is the music of Annette Hanshaw, who made recordings in the 1920's and 30's.  It makes for a strange combination, Indian legend and Jazz Age music, but it works delightfully.

Nina Paley has made Sita Sings the Blues available for download, or you can watch the streaming video at  The artwork is beautiful, and the music is wonderful.  Make yourself comfortable, it's almost an hour and a half long, and worth every minute.

Sita Sings the Blues

Friday, March 13, 2009

Science Literacy Survey

The California Academy of Sciences,, recently conducted a telephone survey of scientific literacy.  There are 6 questions listed on their web site if you want to test yourself - I don't know if they asked other questions or just those 6.

I came across this by way of the links below at and The results of the survey aren't too surprising:  a lot of Americans don't know some very basic facts about the  earth.  However, I was especially interested in the readers' comments left at both of the posts.  I recommend reading them yourself.  A complaint of many was that the questions in the survey don't really measure any understanding of science, but rather they amount to mere trivia.  Understanding science, they argue, requires an understanding of the scientific method, experimental design and generally being skeptical and knowing how to judge the evidence.

Personally, I like (some) trivia.  But I understand the point - it isn't enough to just know some facts.  Given the importance of scientific knowledge and discoveries in everyday life, I think it is important for the public to have an understanding of how scientists figure out how things work.  Advertisers often tout some product as "clinically proven," or "scientifically tested."  The public should know what this means - and I would hope they could make a guess at when it is pure bullshit.

However, I think it is also important to know things.  And for that reason, trivia like the questions asked in the CalAcademy survey are worthwhile.  They probably have little impact on your daily life, but if you are to have any hope at judging the reliablity of what scientists (or politicians or advertisers) have to say, you need to know some of the relevant facts as well.

Science Literacy - American Adults 'Flunk' Basic Science, Says Survey

Boom: So You'd Like To Be An Explosion Scientist

Cool article at  about New Mexico Tech's Energetic Materials Research and Testing Center (EMRTC) in Socorro, NM.  They are even starting a summer "Explosives Camp" for High School students.  I'm jealous!

Cool Science: So You'd Like To Be An Explosion Scientist

Saturday, March 7, 2009

Understanding the Financial Crisis in Everyday Language

We have all heard about the banking crisis and Toxic Assets, but what is it really all about?  This affects everyone and you should be informed - and the regular media doesn't seem inclined to be as clear as they could be.  

This American Life is a radio show on National Public Radio, they have put together a 59 minute program that explains the whole thing in easy to understand language.  I highly recommend listening to the show.


Also, you can get a transcript or download the podcast at This American Life.

Sunday, March 1, 2009

Concertos and Chemistry

Like any specialized field, chemistry has its share of technical jargon, but often technical terms have their roots in more ordinary language.  I like to emphasize the connection between "normal" usage and the more technical use to help my students remember them better.

One example is the "concerted reaction."  In many chemical reactions, more than one thing happens as reactants are transformed into products.  One possibility is these events happen in a set order: step-wise.  Another possibility is that they occur simultaneously and the reaction is said to be concerted.  

The word "concerted"  isn't exactly an everyday word, but it isn't especially unusual.  Wiktionary gives the following definition for concerted:
Performed through a concert of effort; done by agreement or in combination.
Since my students may not be familiar with this usage, I usually make reference to a musical concert, or the concerto form - musicians playing all together.  Certainly "done by agreement," and "in combination." 

The Concerto of Baroque and Classical music typically has a soloist playing with a group of musicians.  Here are two Concertos from different eras.

Antonio Vivaldi is probably best known now for his concertos, in particular The Four Seasons which consist of four of the twelve movements in his opus #8, which in English is entitled: "The Contest between Harmony and Invention."  

The clip below is from a different work than The Four Seasons and features the lute as the solo instrument: Concerto in D Major for Lute.

My second featured concerto is Concerto for Cootie, composed by Duke Ellington.   It was originally composed as an instrumental piece for trumpeter Cootie Williams. Later words were added, the tune may be more familiar as "Do Nothing til You Hear from Me."  This is the instrumental version.