Creation Moment 7/15/2019 - Something Fishy about Evolution

And God said, Let the waters bring forth abundantly the moving creature that hath life,...
Genesis 1:20

"Goldfish underwent whole-genome duplication (WGD) events after they diverged from carp and zebrafish. According to

evolutionary theory, this provided goldfish with extraordinary opportunities for advancement, because now there were two copies of each gene to evolve. One copy, called an “ohnolog” (as a hat tip to Susumi Ohno’s 1970 idea of evolution through gene duplication), could maintain the old functions of a gene. The other copy would be free to undergo evolutionary change. Phys.org explains:

The goldfish (and its cousin the common carp) went through a “whole genome duplication” after evolutionarily “splitting off” from zebrafish. Now, having four copies of every gene instead of two allows for one copy to change and evolve without harming the fish. This can result in lost genes or new functions for genes. This is a natural complement to “knockout” laboratory studies.
Add in the common carp genome with its own ornamental varieties (known as koi), and there are plenty of avenues of comparison to provide researchers with a window into how genes change during evolution.

So how did the genes change?
Chen et al. tell what they found about the goldfish genome in their paper in Science Advances, “De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication.” There are four things a gene can do if it is no longer alone:

• Both copies can be expressed.
• Non-functionalization (non-F): One copy can go silent and not be expressed.
• Sub-functionalization (sub-F): It can take on one of the functions the gene formerly had.
• Neo-functionalization (neo-F): It can evolve a new function.

The first two responses involve loss.
But what about neo-functionalization?
That sounds like gain. It sounds like some new function emerges out of the idle code of the gene copy. Is that what they found?

What Was Gained?

The authors mention “neo-F” 27 times, but readers will look in vain for the key evolutionary words innovation or novel, as in some new, novel function arising that did not exist before. The word gain appears 21 times, but 16 of those appear in the ambiguous form “gain/loss.” So which is it? The paper is filled with jargon and charts, but they obscure the question of what really was gained, if anything. The closest hint of a gain is that an existing gene got switched on in a cell type where it was inactive before:

One ohnolog of the gene scube3 gained new expression in heart, while the other scube3 copy maintained the same expression pattern as that in zebrafish, i.e., neo-F. 

It seems they were most interested in writing statistics about which genes got turned on or off (i.e., which genes were “expressed”). At one point, they say, “We did not distinguish between gain and loss.” The last paragraph of their discussion says:

Several other features of genome sequence evolution affect how gene pairs diverge in expression over time. Key

factors include divergence of the primary genomic sequence through base substitution, gain/loss of exons, and gain/loss of CNEs [conserved noncoding elements], all of which affect gene expression in different ways. Gain/loss of exons is the most important mutation correlated with non-F, neo-F, and sub-F. This process is one that has been proposed to be a critical evolutionary phenomenon that drives vertebrate diversity, and the goldfish–carp speciation is a useful case to explore this evolutionary process.

It sounds like, in the end, they are only repeating the evolutionary dogma that gene duplication gives Darwinism a chance to tinker and create novelty. Neo-functionalization “has been proposed to be a critical evolutionary phenomenon” that drives evolution. It would be “a useful case to explore this evolutionary process.”

Wouldn’t they have highlighted a new gene with some new function if they had found one?"

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