Readers may recall that in the discussion between intelligent design proponents (Dembski, Axe, Gauger) and self-organization proponent James Shapiro, Shapiro replied to Axe and Gauger, who have now replied back ( Evolution News & Views, January 20, 2012):
Background to the discussion here.
We are well aware of the many experimental studies that attempt to draw some conclusion about protein evolution, but we also know that very few of these studies take the critical approach of asking whether the presumed evolutionary mechanism really works. It’s as though most scientists are unwilling to put these fundamental ideas to a serious test.
I can make this point most clearly with a concrete example. We can go into the lab and modify bacterial cells by deleting the entire set of genes dedicated to the synthesis of tryptophan, one of the essential building blocks of proteins. When we observe what happens when these modified cells are given just enough tryptophan to grow and reproduce, we will see lots of things happening, but none that can be expected to reinvent a set of genes for making tryptophan, even in a large population over billions of years.
I know of many processes that people talk about as though they can do the job of inventing new proteins (and of many papers that have resulted from such talk), but when these ideas are pushed to the point of demonstration, they all seem to retreat into the realm of the theoretical.
But of course, as experimentalists we are very willing to see the evidence that might prove us wrong.
Over to Shapiro.