Mutations have been shown to confer a survival advantage to ATP synthase motors in an extremophile. Yet this rotary motor has been a popular illustration for intelligent design. What are we to conclude from the new evidence?
An open-access paper in PNAS shows that part of the rotary motor of ATP synthase — a vital molecular machine for almost all living things — has experienced mutation and selection. We recently featured a dramatic animation of how this motor works. As an exquisite, irreducibly complex device, it looks like evidence par excellence for design. Yet it mutated, and it still works. In the case of alkaliphilic bacterium Bacillus pseudofirmus OF4, it works better with the mutation.

The data indicate a direct connection between the precisely adapted ATP synthase c-ring stoichiometry and its ion-to-ATP ratio on cell physiology, and also demonstrate the bioenergetic challenges and evolutionary adaptation strategies of extremophiles. (Emphasis added.)

Let’s begin with several unquestioned facts:

1. It’s still ATP synthase.
2. The structure and mechanism work the same.
3. The mutated version fits well within known variations of the motor.
4. This bacterium lives in a highly stressed, high-alkaline environment.
5. The unmutated version of the motor works in the bacterium, albeit not as efficiently.
6. The mutation amounts to a substitution of one amino acid for another.
7. ATP synthase is otherwise “highly conserved” from bacteria to humans.
8. The mutation has no bearing on the origin of the machine.

Here’s some background: In the c-ring (the portion of the machine that rotates like a merry-go-round around a central pore), protons attach to c-subunits and drive the rotation so that the other primary domain can synthesize ATP. The number of c-ring subunits varies between species from 5 to 17. This kind of bacterium normally has 12, but the extremophile version has 13.
C-ring subunits contain a conserved motif of glycine repeats (G) in the form GxGxGxG. In Bacillus pseudofirmus OF4, however, the researchers found alanine had replaced the glycine, producing AxAxAxA. This had the effect of creating a 13-subunit ring, with a tighter fit. The modification improved proton pumping, but only in highly alkaline environments (pH > 10). Protons are hard to come by in alkaline environments. Anything that improves the efficiency of utilizing the weakened proton motive force (pmf) would be adaptive.
Glycine and alanine are two of the simplest amino acids. Glycine has a hydrogen (H) for its side group, whereas alanine has a methyl group (CH₃). The codons for the two are also similar. Any of these triplets can code for glycine: GGU, GGC, GGA, and GGG. Any of these triplets can code for alanine: GCU, GCC, GCA, and GCG. It’s clear that a single point mutation, like from GGU to GCU, could switch from one to the other. Such variations within an enzyme are common if they do not destroy function of the enzyme.
Consider the extreme environment of this bacterium. It lives in highly alkaline soils. Any individual with a mutation that improves its ability to extract proton fuel for its motors is likely to proliferate. The mutant is not creating a new function; it’s merely conserving an existing function. The structure and operation of the motor remain the same; the authors said, “several high-resolution structures of isolated rotor rings have demonstrated an overall conserved structural appearance and functionality.” The mutation has the effect of creating a tighter and stabler fit that improves pumping efficiency in the extreme alkaline environment. If it were as effective in more neutral or acidic environments, why would the GxGxGxG motif be so highly conserved?
In other words, because the environment of this bacterium is stressful, extreme conditions call for desperate measures. More importantly, the mutational pathway for its adaptation is simple, well within the “edge of evolution” accessible to natural variation and selection as described by Michael Behe in his book, The Edge of Evolution (2008). Behe described mutational pathways, consisting of one or two mutations, that allow malaria to escape when stressed by chemical agents trying to kill it. He demonstrated that the probability of those lifesaving mutations do not exceed the probabilistic resources available; adding more required mutations, though, quickly exceeds them.
The authors indicated that the mutations they found are within the range of functional variation:

Our data indicate that B. pseudofirmus OF4 can assemble and operate ATP synthases with different stoichiometries of c-rings in the range of c11 to c15, but robust growth at high pH is restricted to strains with a majority of c-rings with at least the c13 stoichiometry.

When protons are in short supply, having more c-ring subunits helps. That’s why this extremophile benefits with the alanine motif, because it adds a subunit and tightens the fit of the c-ring in the membrane. It’s only when the pH gets above 10 that the mutation is beneficial. Otherwise, if it were a generally beneficial change, all species would use it. Instead, the GxGxGxG motif is the conserved form, even in similar bacteria that live in neutral environments.
The authors say that the location of the particular mutation is a mutational hotspot. Other extremophiles are known to have particular variations there. But one cannot mutate these delicate motors willy-nilly:

The changes in the tertiary structure of these mutants have no influence on complex stability with respect to pH, temperature, or detergent, but further mutations finally destabilize the c-ring.

The authors end by stating that this mutation could have spread quickly in the population. With i indicating the number of c-ring subunits, the rate of ATP production is i x pmf (proton motive force). The mutant proliferates because it has a slightly improved production rate of ATP:

The alanine motif is a necessary, but insufficient, adaptation of alkaliphilic Bacillus bacteria. It has a direct influence on the c-ring stoichiometry and its indigenous property to determine the ATP synthase i value, and thus directly modulates the cell’s physiology and bioenergetics, facilitating growth at pH >10. Remarkably, and in agreement with previous work, this observation also suggests that i can be adapted by just one or two selected mutations. This property enables adaptation to new environmental challenges, a process that can occur within a rather short evolutionary time frame.

It’s an interesting paper that demonstrates adaptive selection on a small scale. But since the changes are well within the edge of evolution, since they only affect bacteria in a stressed environment, and since they do not alter the irreducible complexity of functional parts, the findings do not alter the inference to design. If anything, they show the weakness of evolutionary theory. It can only permit small-scale adaptations under special conditions, provided the changes do not destabilize the complex machinery.
And who knows; it could be argued that the “mutational hotspot” that permits this adaptability to environmental challenges was itself designed.