The Achilles’ heel of the modern synthesis, as noted by the philosopher Ron Amundson, 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. Perhaps the most exciting area in evolution is in exploring how rewiring the circuitry of genes produces different arthropod appendages, or wingspots on butterflies.

Eric H. Davidson, a colleague of mine at CalTech, has dissected the network of interactions between the genes that build the gut of sea urchins and starfish during development. When he compares these gene networks, there is a core of about five genes whose interactions are essential to forming the gut, and which have been preserved for some 500 million years.

One advantage developmental biologists have over paleontologists is that they can experiment on the development of these animals. Most of the genes in this network can be removed, and the developing embryo finds a way to compensate. But these five core genes, which form what Davidson calls a kernel, cannot be modified: change any one of them and no embryo forms at all. There is no reason to think that there was anything unusual about how this kernel first evolved some 500 million years ago (before sea urchins and starfish split into different groups), but once the kernel formed it locked development onto a certain path. These events, small and large, limit the range of possibilities on which natural selection can act. These questions about mechanism were not even being asked under the modern synthesis.

The failure to consider how biodiversity grows reflects an even more troubling flaw in the modern synthesis: it lacks any real sense of history. This may sound odd, as evolution is about history. A geologist would describe evolutionary theory as uniformitarian: “The present is the key to the past.” This is the principle we use that by understanding how processes operate today we can understand past events. Evolutionary theory assumes that the processes we can study among fruit flies disporting themselves in a laboratory capture the broad sweep of evolutionary change.

But 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. This can happen in simple ways, as termites construct their own environment by building termite mounds. These mounds may last for dozens or hundreds of years and provide a sort of ecological inheritance for generations of termites.

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.