By comparing the differences in the genes for Vma3 and Vma11, Thornton and his colleagues reconstructed the ancestral gene from which they both evolved. They then used that DNA sequence to create a corresponding protein—in effect, resurrecting an 800-million-year-old protein. The scientists called this protein Anc.3-11—short for ancestor of Vma3 and Vma11. They wondered how the protein ring functioned with this ancestral protein. To find out, they inserted the gene for Anc.3-11 into the DNA of yeast. They also shut down its descendant genes, Vma3 and Vma11. Normally, shutting down the genes for the Vma3 and Vma11 proteins would be fatal because the yeast could no longer make their rings. But Thornton and his co-workers found that the yeast could survive with Anc.3-11 instead. It combined Anc.3-11 with Vma16 to make fully functional rings.
Experiments such as this one allowed the scientists to formulate a hypothesis for how the fungal ring became more complex. Fungi started out with rings made from only two proteins—the same ones found in animals like us. The proteins were versatile, able to bind to themselves or to their partners, joining up to proteins either on their right or on their left. Later the gene for Anc.3-11 duplicated into Vma3 and Vma11. These new proteins kept doing what the old ones had done: they assembled into rings for pumps. But over millions of generations of fungi, they began to mutate. Some of those mutations took away some of their versatility. Vma11, for example, lost the ability to bind to Vma3 on its clockwise side. Vma3 lost the ability to bind to Vma16 on its clockwise side. These mutations did not kill the yeast, because the proteins could still link together into a ring. They were neutral mutations, in other words. But now the ring had to be more complex because it could form successfully only if all three proteins were present and only if they arranged themselves in one pattern.
Thornton and his colleagues have uncovered precisely the kind of evolutionary episode predicted by the zero-force evolutionary law. Over time, life produced more parts—that is, more ring proteins. And then those extra parts began to diverge from one another. The fungi ended up with a more complex structure than their ancestors had. But it did not happen the way Darwin had imagined, with natural selection favoring a series of intermediate forms. Instead the fungal ring degenerated its way into complexity.
Gray has found another example of constructive neutral evolution in the way many species edit their genes. When cells need to make a given protein, they transcribe the DNA of its gene into RNA, the single-stranded counterpart of DNA, and then use special enzymes to replace certain RNA building blocks (called nucleotides) with other ones. RNA editing is essential to many species, including us—the unedited RNA molecules produce proteins that do not work. But there is also something decidedly odd about it. Why don't we just have genes with the correct original sequence, making RNA editing unnecessary?
The scenario that Gray proposes for the evolution of RNA editing goes like this: an enzyme mutates so that it can latch onto RNA and change certain nucleotides. This enzyme does not harm the cell, nor does it help it—at least not at first. Doing no harm, it persists. Later a harmful mutation occurs in a gene. Fortunately, the cell already has the RNA-binding enzyme, which can compensate for this mutation by editing the RNA. It shields the cell from the harm of the mutation, allowing the mutation to get passed down to the next generation and spread throughout the population. The evolution of this RNA-editing enzyme and the mutation it fixed was not driven by natural selection, Gray argues. Instead this extra layer of complexity evolved on its own—“neutrally.” Then, once it became widespread, there was no way to get rid of it.