Thursday, March 26, 2009

What Edison Helped Take from Us

I originally wrote this entry on September 7, 2004, and published it on

Inventions in science and technology are not all about progress.

Every technical invention seems to take something from us in return for what it gives.

With the invention and propagation of basic electric lighting, ultimately brought to every office and home in every city and small town, something sacred was taken from most people--a serene night's sky, which most urbanized people can now see only through the sanitized and limited version that comes to them as images telescopes have viewed, processed and recorded according to their own limitations.

No longer do we need to feel, on a nightly basis, a deep wonder about our place in the universe. The problem has been solved and put to rest.

Tuesday, March 17, 2009

Structural Analysis of Proteins

I wrote this entry, originally, on July 4, 2004.

In a recent paper, computer science professor Yuan-Fang Wang of UC Santa Barbara, describes a tool based on 3-D Java for fast protein visualization.

The 3-D structure of proteins determines their biochemical operation.

For example, a great deal of effort was used to map the 3-D structure of Hemoglobin, the main ingredient of our red blood cells, in order to discover and explain how it fixes oxygen.

Computer visualization is only one aspect of structural analysis. In fact, it is one of the last steps in the the geometric analysis of a protein. (The ultimate goal being the actual biochemical function and relationships.)

Another important (and more fundamental) aspect is the actual determination of the geometric structure given a protein's amino acid sequence.

Such determination involves an optimization problem which searches for geometric positioning of protein backbone such that the lowest potential energy state is attained.

This procedure follows from the basic physical principle that all structures prefer the geometry that leads to the lowest potential energy.

The potential engergy can be determined by adding all potential energies due to interactions among the amino acid molecules that have been strung together in a protein.

There is a whole separate art in writing the potential energy equation as a function of molecular positioning and solving it for its lowest value in the hyperdimensional space of the molecular distances. The optimization problem can be solved in a number of ways. Since this is a large-dimension problem, it is important to use some heuristics to start the problem with the protein geometry in a realistic initial state. Following this initial state, the computation searches for neighboring states that have lower potential energy. This sequence is repeated until lowest potential energy "neighborhood" in the hyper-dimensional space of molecular distance vectors is found.

RoboCup--Robotic Soccer

Robotic soccer has many converts, including Iran, which won the 2nd place in the 2004 German Open's Middle Size league.

There were many German entries, and the first winners come from Osnabruck, Germany, the city of my sister-in-law's family.

RoboCup itself is a larger organization.

At one point, when I was studying with Hubert Dreyfus, I planned to write an essay on whether it was possible for robots to play real soccer.

Well, here is RoboCup's goal: By the year 2050, develop a team of fully autonomous humanoid robots that can win against the human world soccer champion team.

It's a lofty goal, and to what degree it will be accomplished is worth watching.

Unless the robots are allowed to injure people, I doubt they'll win . . .

Now, it is time for me to run for my weekend soccer game on the Stanford compus!

Have a wonderful JavaOne and watch for those robots and don't let them beat you ! ! !