One extra hydrogen bond takes the "random" out of Evolution


GC bias is the tendency for certain regions of a genome to have a higher or lower concentration of guanine (G) and cytosine (C) nucleotides than others. This bias is caused by natural mechanisms outside of NeoDarwinian random mutations.

The three hydrogen bonds between guanine and cytosine (G-C) are the main reason for GC bias. The stronger hydrogen bonding (3) between G-C base pairs makes them more stable than A-T base pairs (2 hydrogen bonds), which means that they are less likely to be denatured by heat or other environmental factors. This makes GC-rich regions of DNA more resistant to mutations and degradation. This means mutations are not random but depend on the increased hydrogen bonding with G:C. NeoDarwinism does not take this into account. Natural mechanisms not random mutations drives change.

In addition, the three hydrogen bonds between G-C base pairs make them more compact than A-T base pairs. This is because the third hydrogen bond between G and C causes them to twist slightly, which brings them closer together. The compactness of GC-rich regions of DNA makes them more difficult to transcribe and replicate, which can also contribute to GC bias.

Finally, the three hydrogen bonds between G-C base pairs make them more likely to be repaired by the cell's DNA repair machinery. This is because the stronger hydrogen bonding makes G-C base pairs more resistant to errors during DNA replication. As a result, GC-rich regions of DNA are less likely to accumulate mutations, which can also contribute to GC bias. Again in contrast to neo darwinisms random mutations.

GC bias is a natural phenomenon that is observed in organisms. It is thought to be a result of the combined effects of the stronger hydrogen bonding, compactness, and repairability of GC-rich regions of DNA without NeoDarwinisms random mutations.

Codon bias is the phenomenon where specific codons are used more often than other synonymous codons during translation of genes. This bias can vary within and among species, and is influenced by a number of factors, including the genome composition, GC content, expression level and length of genes, position and context of codons in the genes, recombination rates, mRNA folding, and tRNA abundance and interactions.

Codon bias can have a significant impact on gene expression and protein folding. For example, genes with a high degree of codon bias are often expressed at higher levels than genes with less bias. This is because the use of optimal codons can help to achieve faster translation rates and higher fidelity.

GC bias drives codon bias in the absence of natural selection. This is because the factors that cause GC bias, such as mutational bias and BGC affects the frequency of synonymous codons. As a result, even if there is natural selective pressure on codon usage, GC bias still leads to a preferential usage of certain synonymous codons without natural selection.

Codon bias is the non-random ( versus NeoDarwinian random)  usage of synonymous codons in a genome.  Codon bias is caused by factors outside of natural selection including:

  • Mutational bias: Some nucleotides are more likely to mutate into other nucleotides than others. This can lead to a bias in the usage of codons that contain these nucleotides.

  • GC-biased gene conversion: This is a type of genetic recombination that is more likely to occur between nucleotides of the same base composition (G or C). This can lead to a bias in the usage of codons that contain more Gs and Cs.

  • Transcriptional factors: Some transcription factors bind to specific sequences of nucleotides in DNA. This can influence the expression of genes, including the choice of codons that are used.

  • RNA secondary structure: The folding of RNA can affect the efficiency of translation. This can lead to a bias in the usage of codons that are less likely to form secondary structures.

In addition to these factors, codon bias can also be influenced by the environment. For example, in bacteria, the availability of certain amino acids can affect the choice of codons that are used epigenetically.

Here are some specific examples of how codon bias can act outside of natural selection:

  • In bacteria, the availability of certain amino acids can affect the choice of codons that are used. For example, if a bacterium is growing in a medium that is low in the amino acid arginine, it will be more likely to use codons for arginine that are translated more efficiently.

  • In plants, codon bias can be influenced by the transcriptional factors that bind to the DNA. For example, a transcription factor that binds to a specific sequence of nucleotides may also bind to other sequences of nucleotides that are similar in base composition. This can lead to a bias in the usage of codons that are located near the binding site of the transcription factor.

  • In viruses, codon bias can be influenced by the host cell. For example, a virus that infects a cell that is low in a certain amino acid may be more likely to use codons for that amino acid that are translated more efficiently.

Codon bias is a source of rapid adaptation in organisms. This is because it can allow organisms to change their gene expression without changing the amino acid sequence of the protein. For example, if an organism is exposed to a new environmental condition, it may need to produce more of a particular protein. If the codon for that protein is biased towards a certain codon, the organism can quickly adapt by mutating the gene to use that codon more often.

This type of rapid adaptation is not possible under the traditional neo-Darwinian model of evolution, which states that evolution occurs through small, gradual changes over time. Codon bias-mediated adaptation is an example of how evolution can occur more rapidly than previously thought.

Codon bias is a powerful tool for rapid adaptation in organisms. It is a mechanism that can allow organisms to change their gene expression quickly in response to new environmental conditions or challenges. This makes codon bias an important factor in evolution and adaptation outside of NeoDarwinism.

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