RNA bias at the "Bush of Life" challenges Neo-Darwinism

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Darwin's drawing verses modern Phylogenetics

The Bush of Life concept is better supported than Darwin's Trees of Life for two main reasons:

  1. Horizontal gene transfer (HGT): HGT is the process of one organism transferring genetic material to another organism that is not its offspring. HGT is common in bacteria and archaea, and it is also known to occur in eukaryotes. HGT can blur the lines of descent between organisms, making it impossible to reconstruct a tree-like evolutionary history.

  2. Incomplete lineage sorting (ILS): ILS occurs when alleles from different ancestral species are still present in a descendant population after speciation. ILS can also make it impossible to reconstruct a tree-like evolutionary history, as it can lead to multiple different evolutionary hypotheses being equally likely.

The bush of life model is a more complex and accurate representation of the evolutionary history of life. It takes into account the fact that HGT and ILS can occur, and it allows for multiple lineages to branch off from the same node simultaneously. 

The BOL model challenges neo-Darwinism by rejecting the idea of a single, linear tree of life. Instead, the BOL model proposes that life evolved in a complex, branching network, with many different groups of organisms emerging simultaneously. This is supported by recent evidence from paleontology and genetics, which has shown that the tree of life is much more complex and interconnected than previously thought under neo-Darwinism.

It shows life began suddenly and "complex" with no intermediates as opposed to NeoDarwinian gradual change.

Phylogenetics shows that RNA was at the base of the bush of life. Phylogenetics is the study of evolutionary relationships between the DNA of organisms, and it is based on the analysis of shared characteristics. One of the strongest pieces of evidence that RNA was at the base of the bush of life is the universal presence of RNA in all living organisms. RNA is essential for many cellular processes, including protein synthesis, gene regulation, and cell signaling. 


RNA phenotypic bias refers to the tendency of RNA sequences to change  in a non-random way, which can make it difficult to reconstruct accurate evolutionary relationships between RNA-containing organisms. This bias can be caused by Mutational bias. RNA molecules are more likely to mutate in certain ways than others as opposed to neo darwinism random mutations. Phenotypic bias refers to the fact that some RNA sequences are more likely to fold into functional structures than others. This can constrain the change of RNA sequences. NeoDarwinisms natural  selection is constrained as it can only act on RNA sequences that can fold into functional structures.

Phylogenetics have shown that RNA molecules go back to the bush of life, meaning that they were present in the ancestors of all living things. 

Here are some specific examples of how RNA phylogenetic bias can affect the reconstruction of evolutionary relationships:

  • Long-branch attraction: Long-branch attraction is a phenomenon in which two distantly related organisms appear to be more closely related to each other than they actually are. This can happen when the RNA sequences of these organisms have changed rapidly.

  • Compositional bias: Compositional bias refers to the fact that RNA sequences often have a non-random distribution of nucleotides. This can make it difficult to accurately align RNA sequences, which can lead to errors in phylogenetic reconstruction.

  • Secondary structure bias: Secondary structure bias refers to the fact that RNA sequences can fold into complex three-dimensional structures. These structures can affect the rate of change of RNA sequences, and can make it difficult to accurately align RNA sequences.

RNA phenotypic bias challenges Neo Darwinism in the following ways:

  • It shows that not all possible phenotypes are equally likely to arise. Neo Darwinism assumes that natural selection acts on all possible phenotypes, but RNA phenotypic bias shows that only a subset of possible RNA structures are likely to arise from biased mutations. This means that natural selection cannot explore the full range of possible phenotypes and could lead to suboptimal adaptations.

  • It suggests that developmental (phenotypic) bias may play a more important role in evolution than previously thought. Developmental bias is the tendency of certain phenotypes to be more likely to arise than others, due to the way that genes are expressed and how proteins interact. RNA phenotypic bias shows that developmental bias can have a strong influence on the shape of the morphospace, the space of all possible phenotypes. This could limit the range of phenotypes that are available to natural selection.

  • It raises the possibility that evolution is not always driven by natural selection. If developmental bias is the primary explanation for the occupation of the RNA morphospace, then it is highly likely some RNA structures arise simply because they are more likely to fold into the correct shape, rather than because they are beneficial to the organism. This could lead to the development  of new traits.

  • The evolution of new RNA genes. Neo Darwinism assumes that new genes arise from random mutations in existing genes. However, RNA phenotypic bias suggests that it may be more difficult for new RNA genes to arise than previously thought. This is because new RNA genes would need to fold into the correct shape in order to be functional. If RNA phenotypic bias is strong, then only a small subset of possible RNA sequences would be likely to fold into functional structures. This would make it difficult for new RNA genes to develop.

  • The evolution of complex RNA structures. Some RNA molecules fold into very complex structures, such as ribosomes and spliceosomes. Neo Darwinism assumes that these complex structures evolved through a series of small, gradual steps. However, RNA phenotypic bias suggests that it may be highly improbable  to evolve complex RNA structures through a series of small mutations. This is because even small changes to the RNA sequence could disrupt the overall fold of the molecule. 

Overall, RNA phenotypic bias suggests that Neo Darwinism may need to be modified or replaced in order to account for the role of developmental bias in evolution. It is still an active area of research, and scientists are still trying to understand the full implications of RNA phenotypic bias for understanding NonDarwinian evolution.

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