The rift in the biological sciences may lie between computational biologists and wet labs, but when we look at individual fields, we see other divisions. In an essay in PLoS Computational Biology Carl Zimmer describes the divide amongst evolutionary biologists. On one side are researchers who like to get their hands dirty -- ecologists, paleontologists, and others that fall under the label 'naturalist'. And on the other side we have the people that prefer to work with molecular tools; Zimmer calls these guys computational biologists, but they also generate their own data, so that label isn't quite correct. The rift between evolutionary biologists essentially boils down to people studying morphological/phenotypic evolution and those studying molecular evolution.
Zimmer points out that this division is quite old -- dating back to the early days of genetics. Only recently have we developed the tools allowing us to bridge that divide. The future of evolutionary research lies not in the study of the evolution of phenotypes or genomes alone, but in research programs that bridge the gap. For example, what are the phenotypic effects of all that copy number polymorphism? The top research labs should view Zimmer's rift as a great opportunity for interdisciplinary research.
See also: Carl Zimmer's blog entry.
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another issue is the difference between those who use molecular evolution as an means (e.g., ecologists) and those who see the study of molecular evolution as an ends (this is the more the computational people). some in the former may dismiss molecular work as 'reductionism,' but many are also quite happy to build upon this 'reductionist' base.
Yes, and some of the arguments over things like "DNA Barcoding" relate to this. Most molecular phylogeny types hate barcoding because the proposed tags are generally not very informative phylogenetically. Many ecologist types don't care, because they aren't interested in making trees; they just want a tool that can distinguish one species from another at the molecular level.