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Even the Cell's Shredder Looks Designed

The more deeply scientists come to appreciate the complexities of molecular machines, the less inclined they seem to talk about evolution.

That's true of an article on PhysOrg about the exosome. This molecular machine, responsible for shredding excess or misformed RNAs, is composed of 10 proteins arranged into a barrel with a slicer at the end. Researchers at the Max Planck Institute in Munich were delighted to see the machine with unprecedented clarity, allowing them to decode its structure and function.

Debora Makino, a postdoctoral researcher in the Research Department led by Elena Conti has now obtained an atomic resolution picture of the complete eukaryotic exosome complex bound to an RNA molecule. The structure of this complex allowed the scientists to understand how the exosome works. "It is quite an elaborate machine: the exosome complex forms a hollow barrel formed by nine different proteins through which RNA molecules are threaded to reach a tenth protein, the catalytic subunit that then shreds the RNA into pieces," says Debora Makino. The barrel is essential for this process because it helps to unwind the RNA and prepares it for shredding. "Cells lacking any of the ten proteins do not survive and this shows that not only the catalytic subunit but also the entire barrel is critical for the function of the exosome," Makino explains. (Emphasis added.)
They have established that this machine is irreducibly complex in eukaryotes. Does it have any evolutionary precursors?
The RNA-binding and threading mechanism used by the exosome in eukaryotes is very similar to that of the exosome in bacteria and archaebacteria that the researchers had structurally characterized in earlier studies. "Although the chemistry of the shredding reaction in eukaryotes is very different from that used in bacteria and archaebacteria, the channeling mechanism of the exosome is conserved, and conceptually similar to the channeling mechanism used by the proteasome, a complex for shredding proteins," says Elena Conti.
With this description in mind, several problems become apparent for evolutionary explanations of these machines. First of all, they are already present in bacteria and archaebacteria, presumably the simplest living things. Moreover, the bacterial exosome is chemically different but structurally similar. This means the design is "conserved" but not the ancestry. Then there is another chemically different but structurally similar machine in eukaryotes: the proteasome.

These machines all appear to be irreducibly complex. They are composed of multiple parts, each essential for function. They are also essential for life: the article says that "unwanted accumulation of RNAs can be damaging to the cell" and that these complex machines have multiple functions. In addition to shredding excess RNAs, the exosome "processes certain RNA molecules into their mature form." Since all living things rely on DNA translation via RNA molecules (messenger RNAs and transfer RNAs), it is difficult to imagine any putative ancestor getting by without functional exosomes from the very beginning. Maybe that's why the article did not even mention evolution.

Wikipedia's entry on the exosome provides only a pitiful stab at a Darwinian explanation. Because some shredders have similar components and structures, they "are thought to be evolutionarily related and have a common ancestor." Are thought by whom? No common ancestor is put forward as a candidate. The only other mention of evolution is in relation to certain ribonuclease domains of the exosome: "The exact nature of these ribonuclease domains has changed across evolution from bacterial to archeal to eukaryotic complexes as various activities have been gained and lost." That's a statement of faith, not a scientific demonstration.

With nothing else to say about evolution, Wikipedia notes, "the structure of the core exosome is highly conserved from archea to humans, suggesting that the complex performs a vital cellular function." Conservation is the opposite of evolution.

The original paper in Nature is similar in approach: no mention of evolution, but repeated mentions of conservation, as in the concluding sentence:

Although the chemistry of the reactions is different, the channeling mechanism of exosome complexes is remarkably conserved from prokaryotes to eukaryotes and parallels the mechanism used by the proteasome to confine and prepare polypeptides for processive degradation.
If the exosome were the only irreducibly complex molecular machine appearing in fully functional form in the simplest life, it would be one big challenge for evolution. Cells, though, are loaded with thousands of other examples. This fact taxes the ability of a blind, unguided process far beyond its breaking point.

The failure of neo-Darwinism is only negative evidence for intelligent design, but the functional complexity in the exosome is positive evidence. We know from uniform experience that only intelligence is capable of ordering disparate parts into complexes that work to accomplish a task essential to a system. When even the cell's shredder shows these qualities, the most logical inference for the whole is design.