Chapter 2 — The Engine Nobody Built

Every bacterium that moves by swimming carries a rotary engine no human engineer designed. The bacterial flagellum is a molecular machine consisting of a rotor, stator, drive shaft, bushings, universal joint, and propeller—all operating at the nanometer scale inside a single cell. In Escherichia coli the flagellar motor spins at up to 100,000 revolutions per minute and can reverse direction in less than a millisecond. It is powered by proton flow across the cell membrane, not by ATP. It self-assembles from the tip outward.

The motor requires approximately 40 proteins working in precise coordination to function. Remove any one of the required proteins and the motor does not function at reduced capacity. It does not function at all. There is no functional intermediate state between non-existent and complete. Michael Behe documented the irreducible complexity of the flagellum in Darwin's Black Box (1996). The argument has not been satisfactorily answered in the decades since.

The evolutionary literature has proposed that some flagellar proteins may derive from a simpler secretion system called the Type III secretion system. This proposal inverts the likely direction of derivation, involves fewer proteins, and does not address the irreducibility of the motor assembly itself. The flagellum either works or it does not. No partial version confers any motility benefit.

Behe, M.J. Darwin's Black Box: The Biochemical Challenge to Evolution. New York: Free Press, 1996. Chapter 3. Berg, H.C. "The rotary motor of bacterial flagella." Annual Review of Biochemistry 72 (2003): 19–54.

Chapter 3 — The Turbine in Every Cell

Every living cell runs on adenosine triphosphate—ATP. ATP powers every energy-requiring process in every cell of every living organism. The molecule that produces the overwhelming majority of cellular ATP is ATP synthase—a molecular turbine six nanometers across. It consists of two linked rotary motors: the F0 subunit embedded in the membrane, driven by proton flow, and the F1 subunit protruding into the cell interior. The rotation of F0 is mechanically coupled to F1, which uses that rotation to synthesize ATP from ADP and inorganic phosphate.

Paul Boyer of UCLA worked out the binding change mechanism over decades of research. John Walker of the MRC Laboratory in Cambridge solved the crystal structure. Hiroyuki Noji's group at Tokyo University directly observed single-molecule rotation. Boyer and Walker shared the 1997 Nobel Prize in Chemistry.

The machine is all or nothing. No partial assembly of ATP synthase produces any ATP. The proton gradient, the mechanical linkage, and the precise geometry of the binding sites must all be present and coordinated. The system that produces the universal energy currency of all life requires full assembly before it produces any function whatsoever.

Boyer, P.D. "The ATP synthase—a splendid molecular machine." Annual Review of Biochemistry 66 (1997): 717–749. Nobel Prize in Chemistry 1997: nobelprize.org. Noji, H., Yasuda, R., Yoshida, M., Kinosita, K. Jr. "Direct observation of the rotation of F1-ATPase." Nature 386 (1997): 299–302.