In your August 1, 2005 issue, Herbert Sauro writes: "Given the statistics on modern chip design, one wonders if, in fact, cellular complexity has been surpassed [by computer technology]. For example, with the recent move to 90-nm fabrication technology, the average transistor is now less than 50 nm in diameter – only 5 times bigger than the average intracellular protein."1 However, proteins are not just static structures of atoms; they also contain dynamic circuits that convey nuclear force and charge, with highly complex nuclear interactions that change not only the shape but also function of the protein. The "transistor" in a protein is often or always an atom.

For example, look at the reaction centers of the photosynthetic light harvesting proteins, which are just 10 nm across – a fifth the size of a single transistor. These proteins contain extensive energy control and switching circuits, in which each individual...

Herbert Sauro responds: I completely agree with Robin Colclough that understanding cell behavior at the atomic level is an incredibly difficult problem, a task I would probably leave to my chemistry colleagues. The comparison I made with man-made devices, however, was on a different level. Although a single enzyme, containing hundreds of amino acids, is indeed a complex entity, it is significant that we can nevertheless often distill its properties down to a simple Michaelis-Menten type equation. In other words the outward behavior of an enzyme is in fact remarkably simple given what's going on inside the enzyme.

Likewise with a transistor, outwardly the response of a transistor is very simple, so simple that we teach it to our high school students. Internally, however, a transistor is quite complex, the flow of electrons, and the changes in the electric field that occur as a transistor switches state is by no means trivial and requires a deep understanding of quantum mechanics. It is this separation of behavioral levels that allows us to comprehend complex systems and I believe it to be one of the distinguishing features of systems biology. At the end of the day what makes something appear to be complex is often our perception. By refocusing our view on a problem we will often see the wood for the trees.

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