The article on the eye greatly oversimplifies what Darwin said about the evolution of the eye. Models for the evolution of eyes have been made too. Its not irreducibly complex.
As for the first article, the bacterial flagellum being irreducibly complex has been pretty throughly debunked. A model for the evolution of the bacterial flagellum was proposed in 2003. Each form is functional and an improvement on the previous form. This model was shown in the Kitzmiller v. Dover trail with absolutely no rebuttal by the intelligent design supporters there.
The Flagellum Unspun
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Who really knows? Who will here proclaim it?
Whence was it produced? Whence came creation?
the One who looks down on it, in the highest heaven, only He knows