Is Darwin due for an upgrade?

I would recommend you have a look at this article by Douglas Erwin (PDF here) on the prospects of a paradigm shift in evolutionary biology. Here are some clips:

...constructed from the 1930s to 1950s by early geneticists, paleontologists and others..the modern synthesis...holds that mutations to DNA create new variants of existing genes within a species. Natural selection, driven by competition for resources, allows the best-adapted individuals to produce the most surviving offspring. So adaptive variants of genes become more common...Computer simulations have shown how selection can produce a complex eye from a simple eyespot in just a few hundred thousand years.

In the past few years every element of this paradigm has been attacked. Concerns about the sources of evolutionary innovation and discoveries about how DNA evolves have led some to propose that mutations, not selection, drive much of evolution, or at least the main episodes of innovation, like the origin of major animal groups, including vertebrates.

Comparative studies of development have illuminated how genes operate, and evolve, and this places less emphasis on the gradual accumulation of small genetic changes emphasized by the modern synthesis. Work in ecology has emphasized the role organisms play in building their own environments, and studies of the fossil record raise questions about the role of competition. The last major challenge has argued for a hierarchical view of evolution, with selection occurring at many levels, including between species.

The Achilles’ heel of the modern synthesis.. is that it deals primarily with the transmission of genes from one generation to the next, but not how genes produce bodies. The recent discoveries in the new field of evolutionary developmental biology, or evo-devo, that the gene Pax-6 controls the formation of eyes in mice and humans, Nkx2.5 heart formation, and a suite of other genes the formation of the nervous system, has provided a means to investigate the genetic and developmental mechanisms influencing how the form of organisms has evolved, not just their genes.

Core gene networks appeared long ago that locked development onto a certain path (an example being a kernel of five key genes regulating development of the gut that appeared 500 million years ago). These events, small and large, limit the range of possibilities on which natural selection can act...just as the erosive power of a river changes the future options for the course of the river, so evolution itself changes future evolutionary possibilities.

The first cyanobacteria turned carbon dioxide into oxygen and set off a revolution that completely changed the chemistry of the oceans and atmosphere. Most species modify their environment and this often changes how selection affects them: they construct, at least in part, their own environment. As evolutionary biologists we have little understanding of what these processes mean for evolution.

Does all this add up to a new modern synthesis? There is certainly no consensus among evolutionary biologists, but development, ecology, genetics and paleontology all provide new perspectives on how evolution operates, and how we should study it. None of these concerns provide a scintilla of hope for creationists, as scientific investigations are already providing new insights into these issues. The foundations for a paradigm shift may be in place, but it may be some time before we see whether a truly novel perspective develops or these tensions are accommodated within an expanded modern synthesis.