Bioengineering and systems biology have one thing in common. Building a more efficient, more robust and more predictable form of life, even to build a cell from scratch. A recent article [1] in the Journal Nature reporting the design of an oxygen binding protein that mimics the effect of hemoglobin, but has a very different structure and is made only using three different amino acids is a marvelous example of why living organisms are not machines and have evolved not by virtue of a designer's intentions, but through trial and error. In the words of the authors:

"... natural selection and evolution build complexity into natural proteins and biological systems. This complexity frustrates biochemists seeking to understand structure and function. ... However common it may be in nature, we maintain that complexity is not an essential feature of protein as a material, nor is it an essential feature of catalysis ... ."

Of course it is not.

Complexity, however, seems to be an essential feature of living things. And the authors proceed to explain their peptide design (a four alpha helical bundle protein with two heme binding sites) and why it has superior quality to natural hemoglobin. The superiority is certainly a matter of opinion. In the words of bioengineers it usually reads like this "exceed natural protein function".

Man made machines are stable. They do not reproduce nor do they grow. Engineering is intelligent design, is the opposite of evolution, although improvement in design do rely on already existing forms that are being improved to fit a function (see Henry Petroski's 'The evolution of useful things'). There is no doubt that man made machines can be superior to life. Think of computers and airplanes and microscopes. But they are not alive. Bioengineering, as artificial selection (breeding, genetic engineering), builds upon the built-in quality of living organisms to change. Ultimately the bioengineer is a designer, works goal oriented and 'facilitates those [properties] that are productive and removes those that are unproductive' [1].

See also Man and Machine / The robot that made itself ... almost / What it takes to make a synthetic cell /

[1] Koder, R. L., J. L. R. Anderson, et al. (2009). "Design and engineering of an O2 transport protein." Nature 458(7236): 305-309.