Kenneth Miller once upon a time said "Never bet against science. You will lose." So, how did the researchers figure it out?
Mitochondria are descended from free-living bacteria, which several billion years ago were swallowed by complex cells. The mitochondria soon became central to the cells’ function.
Mitochondria couldn’t have lasted in their new home without the help of a protein machine called TIM23, which delivers other proteins harvested from the cell’s body. Bacteria don’t possess TIM23, suggesting that it evolved in mitochondria. This seems to pose a cellular chicken-and-egg question: How could protein transport evolve when it was necessary to survive in the first place?
The essential paradox applies to other protein-transporting cell systems, providing disbelievers of evolution with a key part of their critique. As articulated by intelligent design proponent Michael Behe, “This constant, regulated traffic flow in the cell comprises another remarkably complex, irreducible system. All parts must function or the system breaks down.”
According to evolutionary theory, however, cellular complexity is reducible. It requires only that existing components be repurposed, with inevitable mutations providing extra ingredients as needed. Flagella, the hairlike propellers used by bacteria to move, are one example of this. Their component parts are found throughout cells, performing other tasks.
Intelligent design mavens once cited flagella as evidence of their theory. Scientific fact dispelled that illusion. The mitochondria study does the same for protein transport.
When they analyzed the genomes of proteobacteria, the family that spawned the ancestors of mitochondria, Lithgow’s team found two of the protein parts used in mitochondria to make TIM23.There are many other examples of exaptation (Google Scholar showed over 6 thousand papers on the subject). This is another example of how crippling Intelligent Design is as a scientific construct. ID purveyors were content to say that the protein transport was "designed" in place. Real scientists, by continuing to do research, found out otherwise.
The parts are located on bacterial cell membranes, making them ideally positioned for TIM23’s eventual protein-delivering role. Only one other part, a molecule called LivH, would make a rudimentary protein-transporting machine — and LivH is commonly found in proteobacteria.
The process by which parts accumulate until they’re ready to snap together is called preadaptation[or cooption or exaptation].It’s a form of “neutral evolution,” in which the buildup of the parts provides no immediate advantage or disadvantage. Neutral evolution falls outside the descriptions of Charles Darwin. But once the pieces gather, mutation and natural selection can take care of the rest, ultimately resulting in the now-complex form of TIM23.