Natural Selection has not been accurately measured since Darwin

Francis Crick's term "frozen accident" falsely described the seeming rigidity of the genetic code, its apparent inability to accommodate additional amino acids beyond the standard 20. This observation had puzzled scientists for decades, as the genetic code seems to have reached a plateau in its expansion despite the potential for incorporating new amino acids with novel properties.

NeoDarwinian thinking reasoned greater natural selection could occur with more codons.

Several hypotheses were put forward to explain this apparent standstill in the genetic code's evolution. Crick and others  eventually applied natural selection to think redundant codons were neutral as to account for neutral selection.

The question of why the genetic code stopped incorporating new amino acids remained a fascinating topic in evolutionary biology till Cas9 Crispr.

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The redundancy of codons, where multiple codons can specify the same amino acid, has long been considered a neutral feature of the genetic code. This assumption was furthered by Motoo Kimura, who proposed that the presence of redundant codons did not significantly impact the evolutionary trajectory of the code. Kimura developed the Ka/Ks ratio to calculate natural selection. Kimura thought the majority of mutations were "neutral." However, the "selectionists" used his formula for 60 years to prove positive "natural selection."

Ka/Ks ratios, a measure of the relative rates of nonsynonymous (amino acid-altering) and synonymous (silent) substitutions, have been widely used to estimate the strength of natural selection acting on protein-coding genes. Over 60 years tens of thousands of articles used them to "prove" natural selection. The assumption of neutral evolution for redundant codons simplified these calculations to disastrous effect.

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However in just the last few years this question has been solved due to Cas9 Crispr. Recent studies have challenged the strict neutrality of redundant codons, suggesting that they may play a more active role in protein evolution than previously thought. For instance, codon usage bias, the non-random preference for certain codons over others, has been linked to factors such as translation efficiency, protein stability, and gene regulation.

These findings suggest that redundant codons are not merely neutral bystanders but may play a significant role in shaping the evolution of proteins.

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CRISPR/Cas9 is a powerful genome editing tool that has revolutionized our ability to study and manipulate DNA. It is a versatile tool that can be used to make precise changes to the genetic code, including introducing synonymous mutations. Synonymous mutations are changes in the DNA sequence that do not alter the amino acid sequence of the protein that is produced. However, the amino acid sequence is far from the whole story. These mutations were thought to be neutral for 60 years, meaning that they were not thought to have any effect on the organism.

Recent research using CRISPR/Cas9 has shown that synonymous mutations can actually have a significant impact on the fitness of an organism. This fitness is not NeoDarwinian fitness per Ka/Ks rather "real" fitness at the nucleotide level. Ka/Ks is assumed at the population level - huge difference. Plus the Ka/Ks ignores non neutral synonymous mutations. Synonymous mutations can affect the way that genes are transcribed then translated into proteins. NeoDarwinism contemplated translation as a slave to transcription per Cricks "Central Dogma." 

For example, synonymous mutations can change the availability of transfer RNAs (tRNAs), which are small molecules that are essential for translation. This can lead to changes in the rate of protein translation, which can in turn affect the organism's fitness. NeoDarwinism assumed an equal effect of tRNA's at translation.

CRISPR/Cas9 has also been used to study the effects of synonymous mutations on the evolution of proteins. Researchers have found that synonymous mutations can accumulate over time and lead to changes in the protein's folding and function. This suggests that synonymous mutations plays a more important role in protein evolution than previously thought.

Overall, CRISPR/Cas9 has provided new insights into the effects of synonymous mutations. These findings have important implications for our understanding of genetics and evolution.

Here are some specific examples of how CRISPR/Cas9 has been used to study synonymous mutations:

• Researchers have used CRISPR/Cas9 to introduce synonymous mutations into the genes of yeast cells. They have found that these mutations can affect (non neutrally) the yeast's growth rate and ability to survive in different environments.

• Researchers have used CRISPR/Cas9 to study the effects of synonymous mutations on the folding of proteins. They have found that synonymous mutations can change the way that proteins fold, which can affect their function. NeoDarwinism simply assumed protein folding was equal among redundant synonymous substitutions.

• Researchers have used CRISPR/Cas9 to study the effects of synonymous mutations on the evolution of proteins. They have found that synonymous mutations can accumulate over time and lead to changes in the protein's sequence and function.

These are just a few examples of how CRISPR/Cas9 is being used to study synonymous mutations. As our understanding of this tool grows, we can expect to learn even more about the effects of these mutations on genetics and evolution.

As for now neodarwinist's have lost their greatest tool to "assume '' natural selection. 

Indeed as these formulas (eg Ka/Ks) replaced older less accurate formulas, as of date, there really has not been one paper that accurately measured natural selection since Darwin.

After 170 years one can only wonder if there is such a thing.