Self-organization is another evolutionary force that some experts say whips up complex features or behaviors spontaneously in living and non-living matter, and these traits are passed on to offspring through the generations.
"A classic example outside of biology are hurricanes: These are not random air movements at all, but highly organized atmospheric structures that arise spontaneously given the appropriate environmental conditions," Pigliucci said. "There is increasing evidence that living organisms generate some of their complexity during development in an analogous manner."The example given of a spontaneously arising complex structure is protein folding. Proteins take on endless shapes and the mechanism that triggers this form is a chemical signal.
I have always felt that reports like these neglect to explain the distinction between proximate causes and ultimate causes. Proteins do fold spontaneously, but proteins serving a particular function always fold the same way. So in trillions of cells in trillions of different organisms, something is controlling the consistency of the chemical signal and therefore the shape the protein. That something is the gene(s) that codes for the signal. Which means that over time evolution has populated the world with only those genes that code for just the right chemical signal. The process that causes such an accumulation of the right genes is natural selection.
Biologist may not today understand the mechanics of protein folding (proximal causes), but they accept that natural selection has to be the ultimate cause. In this case I feel Massimo Pigliucci fudged the part of ultimate causation and exaggerated the mystery of proximate causation. The level at which such apparent mysteries exists needs to be clarified by the interviewed scientist. It would be too much to expect from the media.