Even recently, the god of the gaps argument is sometimes used. One example is the idea of 'Darwin's black box', the false assertion that the exquisite details of molecular biology cannot be understood in an evolutionary context.
There are two facets of 'god of the gaps' that are particularly bankrupt, one scientific and one theological. Scientifically, god of the gaps is equivalent to suicide, an admission that one simply cannot imagine how to go on any farther. God of the gaps is giving up on science, with no reason to do so. Theologically, god of the gaps means that the realm of god gets smaller each time a gap in our knowledge is filled.
Here, I give two recent examples from my life where the molecular details of evolution have been explicated in greater detail. In neither case are the gaps fully filled - this can never be the case - split a gap in half and we have two smaller gaps. But the gaps are getting sooo small - is it really worth trying to stuff gods in those tiny little gaps?
First, I saw a seminar by Joe Thornton on his work on the evolution of steriod receptors. Joe uses statistical inference to reconstruct the sequence of ancestral proteins. Then he brings them to life in the lab and conducts experiments on the proteins. He is able to reconstruct the order of specific mutations that occurred and that change the function of the proteins he studies.
I found particularly interesting that one particular receptor could identify 3 different steroids at the origin of the protein. Later on, specializations occurred through particular mutations that Joe and his group could identify. When thinking about the evolution of novelty, we often assume that multiple functions are added over evolutionary time. However, Joe's results show how functional complexity can be the original state, and that structural complexity can follow by parsing an ancestral function across subsequently duplicated genes.
To view Joe's presentation, go here.
The second recent example is that a paper from my lab was recently published that reviews our progress on understanding the evolution of the molecular basis of vision (phototransduction). This paper is available for free from the Springer web site.
Todd Oakley and M. Sabrina Pankey (2008) Opening the "Black Box": The genetic and biochemical basis of eye evolution. Evolution Education and Outreach. [Link]