One of ID’s unofficial mascots, the bacterial flagellum, has a counterpart 10 times smaller that also provides strong evidence of intelligent design. Your life — all life — depends on this highly efficient rotary motor. Since its rotary mechanism was first suggested in 1993, details of its exquisite design continue to come to light.
ATP synthase is a rotary motor made of proteins, embedded in the membranes of mitochondria. Plants also have them in their chloroplasts. The two-part machine has a spinning carousel-like rotor labeled F₀ that runs on protons, and a catalytic structure labeled F₁ where ATP synthesis takes place, producing three ATP per cycle. (ATP, adenosine triphosphate, is the universal energy currency of life.) Cells in all kingdoms of life contain this “marvelous rotary engine of the cell” as Yoshida et al. described it in 2001.
A couple of months ago we touched on this fascinating engine in some detail. Since then, four more papers about ATP synthase have been published in the Proceedings of the National Academy of Sciences (PNAS). All of them speak in machine terms (nanomachine, rotation, motor, mechanism, architecture) but none of them have much to say about evolution. They are indications of a major scientific revolution in our time that is transforming the nature of the origins debate. The power is in the details.
Here’s a brief look at the news.
1. Peterson et al., in Comparison of the H⁺/ATP ratios of the H⁺-ATP synthases from yeast and from chloroplast (PNAS June 25, Open Access), worked on figuring out the ratio of protons to ATP produced, comparing results in the mitochondrion of a yeast cell and the chloroplast of a spinach cell. They found that there is a relationship between the number of “c” subunits in the rotor and the number of ATP produced. As previous work showed, it’s not an integer ratio. This suggests that some of the free energy is stored in torsion of the central stalk that acts like a camshaft, transferring the rotation of the F₀ unit to the catalytic F₁ unit. This was the only paper to mention evolution. Look how tentative their “if-then” statement was:

If the c-subunit stoichiometry is the result of an evolutionary pressure, our data give support to the hypothesis that this stoichiometry is one of the key energetic parameters nature can modulate according to the needs of different organisms.

2. Rees et al. focused their attention on the F₁ catalytic region (PNAS, June 25, Open Access). The F₁ portion in cross-section looks like an orange slice with six wedges. Each pair of wedges is a catalytic site where ATP is produced. As the central stalk rotates in 120° increments, the three pairs of wedges are in different stages: accepting ADP plus phosphate, or joining them together, or releasing ATP. In “Structural evidence of a new catalytic intermediate in the pathway of ATP hydrolysis by F₁-ATPase from bovine heart mitochondria,” they described how they isolated the engines from cow heart muscle and watched how the final stage gives birth to an ATP molecule. They found a new intermediate state in the process that provides evidence the ATP molecule leaves phosphate-first. In the paper, they described in detail how the wedges open and close, accepting the ADP and phosphate ingredients “sandwiched” into precise contact “pockets,” with water molecules and magnesium ions moving into specific positions — remarkable for how fast the rotor spins (up to 350 revolutions per second; see PNAS). Rees et al. did not mention evolution.
3. Hakulinen et al. wanted to examine more closely the architecture of intact F₀ (rotor and stator) portions of ATP synthase in bacteria. In “Structural study on the architecture of the bacterial ATP synthase F_o motor” (PNAS June 26, Open Access), they agreed from the start, “F-type ATP synthases are the major supplier of chemically bound energy in the form of ATP in all living cells.” With atomic force microscopy, they resolved some features down to 5 angstroms. A striking projection map shows the rotor c-rings with their 11 parts arranged in tissue with an uncanny resemblance to gears (although the individual motors do not interact). Their images get even better from there, allowing measurements of extensions of parts down to fractions of an nanometer (readers can see them in the open-access paper). Improved resolution is important to understanding how these motors work; this represents a new high water mark in visualization of living engines in some of the simplest of cells. It appears that evolution was the last thing on these researchers’ minds.
4. The most recent paper, by Baker et al. and published July 2 in PNAS, examined some of the lesser-studied parts of ATP synthase: the stator, and other membrane-bound parts. In “Arrangement of subunits in intact mammalian mitochondrial ATP synthase determined by cryo-EM” (not open access), the team imaged intact cow heart ATP synthase at a resolution of 18 angstroms, visualizing the spatial relationships of these key structural parts to the rotor. They also confirmed that the engines produce some curvature in the lipid membranes surrounding them.
Stepping back, we should recall that the study of “molecular machines” is fairly new. After the initial discovery of DNA structure in the 1950s, biologists were still thinking of biochemistry as a specialized kind of chemistry. Only since about the late 1980s did molecular biologists begin to speak of proteins and enzymes as machines. That metaphor has led to a wealth of productive research that is profoundly thought-provoking and suggestive of engineering and design.
We recall Michael Behe expressing, with feeling, this new way of thinking about cellular parts in Unlocking the Mystery of Life: “At the very basis of life, where molecules and cells run the show, we’ve discovered machines — actual machines — literally molecular machines.” Jed Macosko added that there are as many machines as there are functions in a cell. Scott Minnich justified the machine language as beyond mere metaphor: speaking of the bacterial flagellum, he said, “It has a stator, it has a rotor… and they function as these parts of machines. It’s not convenient that we give them these names; that’s truly their function.”
The “molecular machine” revolution coincides with the rise of the intelligent design movement. In 1985, Michael Denton suggested the machine metaphor in Evolution: A Theory in Crisis. Profoundly influenced by that book, Behe in Darwin’s Black Box (1996) proposed the concept of irreducible complexity, giving a shot in the arm to those already questioning the adequacy of Darwinian mechanisms. By the time of the release of Unlocking in 2002, the cat was out of the bag. Everybody, ID supporter or not, had already been talking for years in terms of molecular machines. Even the anti-ID NAS president Bruce Alberts was telling his colleagues in 1998 that to prepare the next generation of molecular biologists, we need to teach them to view the cell as a collection of protein machines; it’s the “biology of the future,” he said.
These papers show that the machine revolution goes on unabated. Sure, some of them mention evolution, and most of the authors probably continue to believe in neo-Darwinism. But look how feeble and useless Darwinian theory is to the core concepts. In the first paper by Peterson, the best they could say was that “if” the rotor is the result of evolutionary pressure, then the proton-to-ATP ratio is one of the key parameters “nature can modulate” according to the needs of the organism. They didn’t say it does. They didn’t tell us how it can. They just tossed out that line as a suggestion and moved back into the machine shop, where the action is.
At an intuitive level, we all know machines are designed. The “molecular machine” revolution can be grasped by laymen and even children. Researchers in the ID field undergird its concepts with the scholarly rigor required of a sound scientific theory. Over time, it seems increasingly likely that exposure to the workings of cellular machines — indeed, to their exquisite perfection — will make clear to all that Darwinism was an unnecessary and useless historical distraction, to be discarded in the rush to understand and imitate the machinery of life.
Image credit: freefotouk/Flickr.