Archive for the 'Molecular Biology' Category

Sep 08 2013

Thoughts on the Immortality of the Crab

The deepest problem: of the immortality of the crab, is that a soul it has, a little soul in fact … That if the crab dies entirely in its totality with it we all die for all of eternity Miguel de Unamuno, ‘The Immortality of the Crab’   Pensar en la inmortalidad del cangrejo (‘Thinking […]

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May 07 2013

The Watussi and the History Erasure Button

The Watussi (or Watusi) was a popular dance craze in the early 1960’s, in addition being the historical name for the Tutsi ethnic group in East Africa. ‘Watussi’ was also the lead track on the seminal offering (Musik von Harmonia) by those legends of Krautrock Michael Rother, Hans-Joachim Roedelius and Dieter Möbius (Harmonia). As I […]

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Mar 28 2013

Remembering the Memorable

One of the features of any network is the appearance of motifs, patterns that recur within a network much more often than expected via any sort of random occurence. The first four notes of Beethoven’s Fifth Symphony are an example of a motif: This opening phrase is one of the most widely recognized in music. […]

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Mar 12 2012

Fruity Loops and Arrowheads

One of the features of any network is the appearance of motifs, patterns (sub-graphs) that recur within a network much more often than expected at random. These small circuits can be considered as simple building blocks from which the network is composed. This analogy is quite useful, since many of these motifs would appear to […]

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Dec 22 2011

Eat Me

Imagine that you are the owner of a small factory that makes replacement windows. Normally, your ordering department does a pretty good job of things and the supply of the constituent parts necessary to make a decent replacement window (one assumes these to be things like glass, vinyl, aluminum, hardware, etc.) arrive punctually and in […]

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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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Sep 12 2011

Transposable elements

DNA sequencing is not static. A considerable amount of DNA jumps around from place to place. While other elements compete for representation at a given locus, transposable elements accumulate by copying themselves to new locations in the genome. Transposable elements are sequences of DNA that can move around to different positions within the genome of […]

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Mar 15 2011

Carbohydrates: More than just calories

Carbohydrates comprise only about 1 percent of the human body; proteins comprise 15 percent, fatty substances 15 percent and inorganic substances 5 percent (the rest being water). Nevertheless, carbohydrates are important constituents of the human diet, accounting for a high percentage of the calories consumed. Thus some 40 percent of the calorie intake of Americans […]

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