V-ATPase proton pump and biological complexity

By Mathew Goldstein

Vacuolar-type H+-ATPase (V-ATPase) is a highly conserved evolutionarily ancient enzyme. A proton pump is an integral membrane protein that is capable of moving protons across a cell membrane, mitochondrion, or other organelle. The V-ATPase proton pump helps maintain the proper acidity of compartments within the cell. The pump has a ring that is made up of a total of six copies of two different proteins, but in fungi a third type of protein has been incorporated into the complex. There are many molecular machines like this in cells. Theists assert that these molecular machines are irreducibly complex and therefore must have been created by a god (a.k.a. Intelligent Designer). How could a ring that consists of three different proteins be created without an Intelligent Designer?

A team of scientists from the University of Chicago and the University of Oregon worked out an answer: "It's counterintuitive but simple: complexity increased because protein functions were lost, not gained," The lead author of the study, Dr. Thornton said. "Just as in society, complexity increases when individuals and institutions forget how to be generalists and come to depend on specialists with increasingly narrow capacities."

Hundreds of millions years ago the proton pump ring consisted of two proteins, similar to those found in animals today. However, these older versions of the protein were more versatile, their functionality was broader than the equivelant proteins seen today so they could substitute for each other in the ring. A gene coding for one of the subunits of the older two-protein ring was duplicated, and the daughter genes then diverged on their own evolutionary paths. The functions of the ancestral proteins were partitioned among the duplicate copies, and the increase in complexity was due to complementary loss of ancestral functions rather than gaining new ones. In other words, since the proteins were now assembled by different genes, the proteins diverged, becoming more specialized.

"The mechanisms for this increase in complexity are incredibly simple, common occurrences," Thornton said. "Gene duplications happen frequently in cells, and it's easy for errors in copying to DNA to knock out a protein's ability to interact with certain partners. It's not as if evolution needed to happen upon some special combination of 100 mutations that created some complicated new function.". Thornton proposes that the accumulation of simple, degenerative changes over long periods of times could have created many of the complex molecular machines present in organisms today. Such a mechanism argues against the intelligent design concept of "irreducible complexity," the claim that molecular machines are too complicated to have formed stepwise through evolution. "I expect that when more studies like this are done, a similar dynamic will be observed for the evolution of many molecular complexes," Thornton said. "These really aren't like precision-engineered machines at all," he added. "They're groups of molecules that happen to stick to each other, cobbled together during evolution by tinkering, degradation, and good luck, and preserved because they helped our ancestors to survive."