Archive for the 'Information Theory' Category

Dec 10 2012


Wikipedia is an amazing online resource for reliable information. Most of the time. In general, Wikipedia is most reliable when the entries are devoted to technical topics for which there is little controversy or a minimum of divergent opinion. Entries that are devoted to topics which may have minority opinions that diverge from the currently […]

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Dec 18 2011


A quodlibet is a piece of music combining several different melodies, usually popular tunes, in counterpoint and often a light-hearted, humorous manner. The term is Latin, meaning “whatever” or literally, “what pleases.” Quodlibet (QUOD) is a suite of network creation, editing and querying software I am currenty developing. QUOD is a software application that displays […]

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Nov 12 2011

Beautiful Data

It has been said that if one really wants to learn something, they should teach it. However we may want to expand that aphorism, to perhaps if one really wants to learn something, they should teach it, organize it or animate it. The commonality between science and art is in trying to see profoundly – […]

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Oct 12 2011

Walking on Eggshells

After a self-declared coding holiday, I was back at things this weekend working on the Pathscrubber module of the Datapunk platform. A recently developed vexing problem that needed to be addressed was actually two problems intertwined. If you used Pathscrubber and clicked on any gene/protein node, PS would query Entrez-gene for the descriptive text and […]

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Jun 18 2011

Genetics as an Interactive Sport

“For your information, I would like to ask a question.” —Samuel Goldwyn From an evolutionary point of view, in order for something to carry information, there must first be some sort of “receiver” that reacts to the source of information and interprets it. Through its reaction and interpretation, the receiver’s functional state is changed in […]

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Dec 02 2010

The Recipe Inside the Recipe

An insignificant percentage of the total amount of DNA is devoted actual gene function. But as with most techniques, it’s not what you have, but rather what you do with it.

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Nov 20 2010

How Things Happen

Emergent processes, such as self-organization, literally create order out of disorder. They are responsible for most of the patterns, structures and orderly arrangements that we find in the natural world, and many of those in the realms of mind, society and culture. Patterns form from a state of non-equilibrium, according to the laws of thermodynamics.

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Oct 31 2010

The Game of Life

Fifty years ago, if a group of scientists were asked to define the key to life, the great majority would point to metabolism; how we obtain energy from food. However, adding all the required molecular components and stirring it up will not produce an organism. A more modern view of molecular biology is concerned with organization in time and space. How doe the molecules of life arrange themselves throughout the cell’s compartments, how do they move around, and communicate so as to synchronize their actions? We can ask this question because we can now inspect the working cell at a molecular level and take snapshots of its molecules doing their business.

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Oct 11 2010

Biofilms and New Music

Many bacteria are capable of altering their genetic expression based upon an assessment of their environmental conditions and a novel approach to controlling bacterial infection may involve interfering with the ability of one bacteria to communicate with another. Interestingly, their modus operandi also makes good New Age music.

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