Back to David's theory of evolution: God's error corrections (Evolution)

by David Turell , Thursday, September 17, 2020, 01:02 (1527 days ago) @ David Turell

The ID view of this subject:

https://evolutionnews.org/2020/09/in-cells-proofreading-and-repair-testify-to-intellige...

" As these new research papers show, the machines involved show exquisite craftsmanship and efficient action to keep other parts — machines outside their own structural needs — humming along.

"How can they do that? How do they know? Such things do not just appear by blind material processes. Proofreading and repair systems had to be operational from the beginning of life, because considering the lethal consequences without them, it’s hard to conceive of any primitive organism surviving, let alone progressing up an evolutionary ladder.

"Before cells divide, billions of DNA base pairs must be precisely duplicated. About one time in 10 million, a wrong base is inserted into the copy. Researchers at North Carolina State University found “genome guardians” that “stop and reel in DNA” during this important operation. Two enzymes cooperate to proofread the copy. They halt the duplication when a mismatch is found until more machines can fix the error.

"A pair of proteins known as MutS and MutL work together to initiate repair of these mismatches. MutS slides along the newly created side of the DNA strand after it’s replicated, proofreading it. When it finds a mismatch, it locks into place at the site of the error and recruits MutL to come and join it. MutL marks the newly formed DNA strand as defective and signals a different protein to gobble up the portion of the DNA containing the error. Then the nucleotide matching starts over, filling the gap again. The entire process reduces replication errors around a thousand-fold, serving as one of our body’s best defenses against genetic mutations that can lead to cancer.

"When cells divide, double-stranded breaks can occur. These are particularly dangerous, often associated with cancer. Medical researchers at University of Texas Health in San Antonio confirm that DNA repair requires multiple tools. Drs. Daley, Sung, and Burma at UT knew that the repair operation, called homologous recombination, is done by resection enzymes, but they were curious why so many different enzymes were involved. Why does the cell “need three or four different enzymes that seem to accomplish the same task in repairing double-strand breaks”? The “perceived redundancy,” they concluded, “is really a very naïve notion.” Like a skilled workman, the cell maintains “An array of tools, each one finely tuned.”

"Another type of error can occur when a gene is being transcribed. If RNA polymerase (RNAP, the transcribing machine) hits a lesion caused by UV radiation or some other mutagen, the transcription can stall. Thankfully, there is a programmed response called transcription-coupled nucleotide excision repair (TC-NER) that knows what to do. That’s a good thing, because faulty repair can lead to “the severe neurological disorder Cockayne syndrome,”

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"The cell has mechanisms for preventing errors, too. Research “has unraveled for the first time the three-dimensional structure and mechanism of a complex enzyme that protects cells from constant DNA damage,...

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"DNA polymerase ζ is the crucial enzyme that allows cells to battle the more than 100,000 DNA-damaging events that occur daily from normal metabolic activities and environmental intrusions like ultraviolet light, ionizing radiation, and industrial carcinogens.

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"Chemical lesions in the genetic material DNA can have catastrophic consequences for cells, and even for the organism concerned. This explains why the efficient identification and rapid repair of DNA damage is vital for survival. DNA-protein crosslinks (DPCs), which are formed when proteins are adventitiously attached to DNA, are particularly harmful. DPCs are removed by the action of a dedicated enzyme — the protease SPRTN — which cleaves the bond between the protein and the DNA.

"DPCs can occur during natural metabolism or by contact with synthetic chemicals. SPRTN has a challenging job, they say, because it must be able to tackle a variety of situations; “the enzyme has to be able to identify many different structures as aberrant.” Its two domains must engage for it to recognize the error and fix it. Julian Stingele explains this fail-safe system:

"One binds to double-stranded, and the other to single-stranded DNA. “So the protein uses a modular system for substrate recognition. Only when both domains are engaged is the enzyme active — and DNA in which double-stranded and single-stranded regions occur in close proximity is often found in the vicinity of crosslinks,” says Stingele.

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"Each system must first recognize the error and then know what to do; otherwise, the consequences can be catastrophic. In each case, the machinery is well designed and finely tuned to solve the problem, and it does so rapidly and efficiently. That takes foresight, and foresight implies intelligent design. As Marcos Eberlin says in his book Foresight: How the Chemistry of Life Reveals Planning and Purpose, “This act of anticipation — foresight — is not a characteristic of blind material processes. It is an act of intelligence, of a mind.'”

Comment: In view of this repair complexity, the idea that God might have wanted the errors to add to diversity is laughable. He seriously didn't want them to the point of designing repair systems as complex as the living systems