Most of these points rely on the belief that evolution is always made up of slow, small changes in the genetic code. While this is the case most of the time (and enables the fine tuning that we see in many species), evolution can happen very quickly.

Population bottlenecks cause species that were once very fit to no longer be fit for an environment, enabling vastly different organisms to become dominant very quickly.

Then there are phenomena like Chromothripsis[1] (only discovered last year), whereby the genetic code of a cell is literally smashed into thousands of pieces and seemingly randomly reassembled. No one is saying that Chromothripsis is a major driver of evolution, but it is interesting in that massive rearrangements of this nature can still provide cells capable of reproducing. In the case of cancer, where it was first discovered, these cells are even able to reproduce faster than normal cells.

The other thing is that even advanced life like mammals and humans have more than 10 times as many bacterial cells than human cells[2]. Since bacteria can evolve very quickly, they play a very important role in evolution.

The eyes from no eyes makes no sense to me, since the entire array of light sensing capabilities are seen in nature. From eagles to plants. The same is true for many of the examples of emergent complexity that are thrown out there.

[1] http://en.wikipedia.org/wiki/Chromothripsis

[2] http://www.scientificamerican.com/article.cfm?id=strange-but...