More about how evolution works: more on patterns (Evolution)

by David Turell , Sunday, October 30, 2016, 23:06 (2944 days ago) @ David Turell

This article describes patterns in gene relationships:

https://www.quantamagazine.org/20161025-pairwise-gene-removal-reveals-genetic-structure/

"Boone, Andrews and a large team of collaborators have published in Science a sprawling report on the nearly two-decade-long set of experiments. In all, they found 550,000 pairs that, when removed, result in sickness or death. This network of genetic connections reveals a previously hidden scaffolding that underlies the operation of the cell. “The complete picture,” Boone said, “clearly shows a beautiful hierarchical structure.”

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"For those of us who are not scientists, the research also provides an interesting reminder that the cell is not as simple as it might seem. Just because a gene is not one of the “essential” 1,200 does not mean it’s unimportant. It simply means that evolution has built many overlapping systems into the cell so that if one part goes, the whole thing doesn’t fall apart.

"For example, the cell has a couple of different pathways that it can use to repair DNA. “Neither one is essential,” said Chad Myers, a computational biologist at the University of Minnesota who is a lead author of the new paper. But if you knock a single gene out in both of those pathways at the same time, “you’ll kill the cell,” he said. With both of those options for DNA repair gone, the cell can’t keep going.

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"Botstein said, “flexibility is the issue in survival — the ability to switch between circumstances that are good, or bad, or whatever, and not die.” Evolution has honed yeast to be ready for many kinds of situations, from the warm surface of a Napa Valley grape to the desert where a bird, having consumed the grape, might deposit it inside its droppings. If the experiments were repeated in myriad other circumstances, the removal of other combinations of genes would be deadly. Those experiments would reveal overlapping  groups of genes that are essential for each of these situations, intimating the immense permutations that life is prepared for.

"The yeast experiments... make clear that the cell is a system where a handful of small changes can add up to a problem, though none of the individual alterations are harmful in and of themselves.

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"In 2013, Claire Moore, a biochemist at Tufts University, received an email from Boone.

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"Moore was vaguely aware of Boone’s work, but didn’t know him personally. “I get this email out of the blue,” she recalled. It said that Boone’s team had identified a gene that might be involved in polyadenylation. Could she check it out for them? “That was a surprise to me,” she said, “because I thought that we had identified all the proteins that did this.”

"But Boone, Andrews and their collaborators had found that this gene, one of the essential, still-mysterious six, had very strong connections with those involved in polyadenylation. It was a simple matter for Moore to see whether knocking it out would interfere with the process in her yeast. And, lo and behold, it did. They had identified the mysterious gene’s function, merely by looking at a database of its relationships, and seeing what happened in the lab.

"Moore, whose findings about the new polyadenylation gene appear in the Science paper, said that she thinks her experience shows the value of the network approach. “For us it’s opened up a whole new direction for the lab,” she said. “I don’t think we would have ever stumbled across it [otherwise].'”

Comment: This arrangement of patterns of gene relationships shows how intricately the genome is constructed to aid in survivability. Note the antibiotic study in which bacteria found a way to overcome the antibiotic. It is very difficult to see how chance evolution developed this intricacy. It looks planned to me. This fits with Wagner's finding of patterns that allow for innovation.