As my friend Jeff used to say (in his best Peter Lorre imitation):

"All I need now . . .is a brain."

For the mad scientist in everyone, here are a few interesting bits and pieces I've found along the way:

PROTEINS

At this time, it's pretty much impossible to figure out how to design a protein to be, for example, more thermostable or more active in the presence of organic solvent. As a result, researchers like Frances Arnold at Caltech have turned to stochastic methods (so-called "Directed Evolution") to generate proteins with new, desirable characteristics.

Some other great work is being done by Kim Janda's group at The Scripps Research Institute in San Diego. I first became interested in his group after reading about some of the work they've done with catalytic antibodies. It's an idea that has its roots in the ideas of Pauling and that came to fruition in the mid-1980s. Many, many years ago, Linus Pauling suggested that enzymes are able to catalyze the chemical processes of the cell by stabilizing the transition state of their respective reaction. Lerner et al. set out to test this idea by generating antibodies that would bind to molecules that mimic the transition states of various reactions. When you allow these antibodies to interact with the reactants instead of the transition state analogs, you do in fact observe catalysis. It's beautiful.

The Protein Folding Problem (being able to figure out how a protein will fold, given just its amino acid sequence) remains beyond our reach. It has been noted, however, that the number of different folds appears to be significantly smaller than the number of different families of proteins. So, the idea of "threading" new sequences onto known structures was developed. Unlike traditional homology modeling, threading pays little attention to the names of the amino acids and instead focuses more on their chemical behavior (polarity, whether they like being buried, whether they like particular types of secondary structure, etc.).

George Rose's group at Johns Hopkins has developed LINUS, an algorithm for ab initio structure prediction, with some promising results. George Rose has also written some interesting reviews on the subject of protein folding, discussing topics such as stability vs. specificity.

 

TRANSPORTATION

I haven't had much occasion to use it of late, but you can read about my electric bike project. I'll try to scan my photos in soon.

One of my dreams is to someday win the deciMach Prize, an award for the first team to create a human-powered vehicle to reach Mach 0.1 (75 mph).

There's also some interesting stuff at the International Human Powered Vehicle Association's web site.

 

ENERGY

Biodiesel is a renewable substitute for petroleum-derived diesel. It is produced by converting triglycerides into glycerol plus three methyl or ethyl esters. The triglycerides can come from any number of sources, including plants (corn, soy, canola) grown especially for biodiesel production, waste fat from butchering animals, and waste cooking oil from restaurants.

Hydrogen fuel cells provide clean, quiet electricity. The hydrogen can come from any number of renewable or nonrenewable sources, and the fuel cell system can be made small enough to make a fuel cell-powered automobile possible.

Lightweight flywheels made of carbon composites are being developed for use as mechanical (well, electromechanical) batteries. One of the nice things about them is that they can accept large pulses of energy (such as that resulting from regenerative braking) more efficiently than traditional chemical batteries.

MISCELLANEOUS COOL STUFF

Science rules! Much to my dismay, I recently discovered that the final episode of Bill Nye the Science Guy was filmed last year. I am in mourning.

Perfluorochemicals are a class of fluids that can hold large quantities of dissolved gases -- enough that you can breathe these fluids instead of gaseous air. If you saw the movie "The Abyss" you've (supposedly) seen this stuff.

When people talk about biological computing, they are usually talking about using biological molecules as switches to replace transistors. But Leonard Adleman has used PCR to devise a wonderfully elegant biological computer that can evaluate combinatorial problems (like The Traveling Salesman problem). He recognized that biological molecules are capable of much more than storing a bit of information.

Sonoluminescence is a remarkable phenomenon in which light can be produced by transmitting high amplitude, high frequency sound through water. You seem to get cavitation in the areas of rarefaction, and when the bubbles collapse there's a huge amount of energy involved. It's estimated that the site of collapse reaches millions of degrees, and it results in a bright flash of light. Best of all, you can even do it in your own home (and no, you don't need to spend $1200 on a kit!).

 

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