Re: Has molecular biology changed the nature of evolutionary thought?

To a large extent I would say that the answer to your question is "no." But 
that would have to be a qualified "no." If we go back to "On the Origin of 
Species" we find that Darwin realized that somehow traits of the parents 
were influencing the traits of offspring. He suspected that the correlation 
was due to some manner of inheritance, but he came to this conclusion 
without any knowledge of genetics, which had yet to be discovered back in 
1859. So the use of the tools of molecular biology has allowed scientists 
to flesh out Darwin's ideas with molecular details. That being said, 
perusal of the major evolutionary biology journals will indicate that most 
of the questions being asked are not that far removed from points raised in 
"Origin." Most investigations are still concerned with documenting how 
population and environmental processes influence the physical makeup (be it 
gene frequencies, femur lengths, brain mass, etc.) of individuals over 
multiple generations. The population parameters being assayed, such as 
effective population size, migration rates, mating biases, and others, were 
all discussed by Darwin. The use of molecular assays and the data they 
provide has brought to this field the ability to investigate evolutionary 
questions at very detailed levels.

One area of investigation that would not exist without molecular biology is 
the study of rates of mutation and substitution. This field got its start 
when protein polymorphism was first assayed in starch gels and remarkable 
levels of polymorphism were found. This, when connected with information 
about how DNA codes for proteins, led to the concept of neutral mutation 
and instigated the Selection vs. Neutrality debate that has raged on and 
off for the past ~40 years. Neutral evolution wasn't an entirely new 
concept, however, as Darwin did realize that many of the changes seen 
between generations were not necessarily under the influence of natural 
selection.