Biological complexity: how a molecular machine is assembled (Introduction)

by David Turell , Wednesday, March 21, 2018, 22:08 (2221 days ago) @ David Turell

It is irreducibly complex and must be designed:

https://evolutionnews.org/2018/03/irreducible-complexity-in-molecular-machine-assembly/

"We know that many molecular machines are irreducibly complex (IC) in their operation. Even more IC is the process of assembling them in the cell. A good example of this is the process of building our good old standby machine, ATP synthase.

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"In a companion Commentary on PNAS, three scientists (Song, Pfanner and Becker) put it bluntly: “The assembly of the mitochondrial ATP synthase is a complicated process that involves the coordinated association of mitochondrially and nuclear encoded subunits.”

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"Whether or not you can follow the jargon is not as important as what they witnessed: an “elegant” process that requires precise timing and coordination. Different machine parts must arrive on schedule, and assemble into intermediate (vestigial) forms that are nonfunctional alone. An inhibitor protein makes sure the machine doesn’t switch on ahead of schedule. The proton-conducting channel has to form just right so that it doesn’t “leak” protons. Only when all the parts are ready does the machine begin to rotate, but even then, the work isn’t complete. Another player is “added to the assembly line” to position the machines on the folds of the mitochondrial membrane (called cristae) at precise angles and spacings for optimum productivity.

"The parts must arrive at the construction site on time. Some of them come from the nucleus, which must seem like many miles away at the scale of the machine. Some are built locally by genes within the mitochondrial genome. Interestingly, there are differences between yeast and humans regarding which genes are encoded where, and in what order they are assembled. But the proof of the pudding is in the respiration after eating: both versions of the machine work efficiently for their respective organisms.

"The intermediate structure, somewhat like a scaffold on which the machine will be built, is also irreducibly complex:We have shown that the assembly of human ATP synthase in the inner organellar membrane involves the formation of a monomeric intermediate made from 25 nuclear-encoded proteins into which the two mitochondrially encoded subunits are inserted and then sealed by association of another nuclear-encoded protein, thereby dimerizing the complex. Association of a final nuclear protein oligomerizes the dimers back-to-face along the cristae edges.

"Notice that parts from the different genomes have to work tightly together. It’s like a manufacturing plant receiving parts locally and from India that have to meet agreed-on specifications to match. There are also rules for import, just like for parts arriving from a far country. The nuclear-encoded parts have to pass through two distinct checkpoints (the inner and outer membranes of the mitochondrion), which each have their robotic security personnel to validate them and facilitate their transport to the inside.

"Previous work has shown how the completed “factory” of machines is organized within the mitochondrion. A specific nuclear protein seals them in two’s (dimers) at an angle, such that the rotating F0 proton pumps can maximize the intake of proton fuel, while the F1 parts, where ATP synthesis occurs, are farther apart to not crowd the output molecules. A “final nuclear protein” joins the dimers together (oligomerizes them) along the membrane edges. The longitudinal spacing is also tightly controlled, so that they don’t crowd each other. Every point of the assembly is programmatically directed. When everything is completed, rows of ATP synthase motors are arranged like turbines in a hydroelectric plant, feeding off a flow of protons produced by upstream machines in the respiration transport chain."

Comment: I have not reproduced the actual quotes from the actual paper, but these simple explanations. All of this is taking place in the mitochondrion where respiration and energy use is handled. This cannot be assembled by chance. It is a complex design and the assembly has to be choreographed by forces that shepherd the construction, and those forces must also be designed. Only God can do this.