Difficulties replicating Kashtan & Alon (2005)

I love the paper, its about the evolution of neural structure. Do brains have parts? Do bodies have parts? If you think so, you’re very forward thinking, because science has no idea how that could possibly have evolved. Kashtan and Alon published a mechanism for the evolution of structure. They proposed that if environments have modular structure then things that evolve in them will as well. Or something like that.
I had trouble replicating their result. By the time I did, I had lost all faith in it. There are some tricks to make the effect seem bigger than it is, and there might be some confounds, though I stopped short of proving it. I’ve got a proposal all written up, but I changed disciplines before I could implement. I’m not the only one who couldn’t replicate — I’ve met others who had the same problem.
I still love that paper, but I personally believe that the mystery of evolved structure is more unsolved than we think.