De Novo genes challenge NeoDarwinism

“the probability that a functional protein would appear de novo by random association of amino acids is practically zero” - Nobel Laureate Jacob Monad, "Evolution and Tinkering”

The existence of de novo genes poses a challenge to NeoDarwinism, because NeoDarwinism traditionally focuses on the evolution of existing genes. NeoDarwinism explains how existing genes can change over time to produce new traits, but it does not explain how new genes can arise from scratch.

The article: "The Origins and Functions of De Novo Genes: Against All Odds?" by Caroline Weisman discusses denovo genes.

De novo genes are genes that arise from previously non-genic DNA. This process seems extraordinarily unlikely, because it seems that random sequence would produce a functional gene only rarely. This is because NeoDarwinian natural selection does not work on non-coding dna only coding DNA. 

However, there is now growing evidence that de novo gene birth is a real and significant phenomenon.

In her review article, Caroline Weisman summarizes what is known about the origins and functions of de novo genes, and discusses how they might arise despite the seemingly low odds. She first discusses three premises that seem intuitively true about genetic material, and which underlie the assumption that de novo gene birth is impossible:

  1. Sparsity: Almost all of sequence space produces no beneficial biological effect under NeoDarwinism.

  2. Fair play: Non-genic sequences are a random sample of sequence space.

  3. Limited trials: Evolution can only sample a modest proportion of non-genic sequences for biological effects.

If de novo genes do in fact exist, Weisman argues that they must do so by violating NeoDarwinism on one or more of these premises. She then goes on to discuss some examples of de novo genes, and what they can tell us about how these genes might arise.

Origins of de novo genes

Weisman begins by discussing the origins of de novo genes. She notes that there are two main ways in which de novo genes can arise:

  1. From NonDarwinian transposable elements: Transposable elements are mobile DNA sequences that can insert themselves into new locations in the genome. When a transposable element inserts into a non-genic region, it can sometimes create a new gene.

  2. From NonDarwinian non-coding RNA: Non-coding RNA is RNA that does not code for proteins. However, some non-coding RNAs can acquire protein-coding potential through mutations. Although this violates the central dogma.

Weisman then goes on to discuss some specific examples of de novo genes that have been identified. One example is the AFGP gene, which is found in gadid fishes. The AFGP gene is thought to have arisen from a transposable element about 3 million years ago. Another example is the MDF1 gene, which is found in yeast. The MDF1 gene is thought to have arisen from a non-coding RNA.

Functions of de novo genes

Weisman then discusses the functions of de novo genes. She notes that de novo genes can have a wide range of functions, including:

  • Regulatory functions: De novo genes can regulate the expression of other genes.

  • Coding functions: De novo genes can code for proteins that have a variety of functions, including metabolism, cell signaling, and immunity.

Weisman also notes that de novo genes can play important roles in NonDarwinian evolution. For example, de novo genes have been implicated in the NonDarwinian evolution of new species and the development of new adaptations.

How do de novo genes arise despite the odds?

Weisman concludes by discussing how de novo genes might arise despite the seemingly low odds. She argues that de novo genes may be more common than previously thought, and that they may arise more easily than we think.

One way in which de novo genes may arise more easily than we think is that they may not need to be perfect to be functional. For example, a de novo gene may only need to code for a small protein domain in order to be functional. Additionally, de novo genes may be able to acquire new functions over time through mutations, although mutations in noncoding DNA are not under natural selection.

Another way in which de novo genes may arise more easily than we think is that they may be able to take advantage of existing cellular machinery. For example, a de novo gene may be able to use existing promoters and enhancers to regulate its expression. However promoter CpG nucleotides are noncoding DNA not under selection. Additionally, a de novo gene may be able to use existing ribosomes and tRNAs to translate its mRNA into protein.

Conclusion

De novo genes are a fascinating topic of research. They are a reminder that evolution is a creative process, and that new genes can arise from unexpected places. However calling evolution a "creative process" implies "agency" something NeoDarwinism specifically denies. Study of de novo genes is helping us to understand how NonDarwinian evolution works, and how new adaptations arise.

Discussion

Weisman's review article provides a comprehensive and up-to-date overview of the research on de novo genes. She does a good job of explaining the challenges involved in studying de novo genes, and she discusses the different ways in which de novo genes might arise.

One of the most interesting points that Weisman makes is that de novo genes may be more common than previously thought. This is supported by the fact that there are now many well-characterized examples of de novo genes, and by the fact that de novo genes have been identified in a wide range of organisms.

Weisman also makes the important point that de novo genes can have a wide range of functions, including both regulatory and coding functions.

How De Novo Genes Challenge NeoDarwinism

NeoDarwinism is a waining theory of evolution.

NeoDarwinism explains how existing genes can change over time to produce new traits. However, it does not explain how new genes can arise from scratch.

De novo genes are a challenge to NeoDarwinism because they show that new genes can arise from non-genic DNA. This means that evolution is not limited to the modification of existing genes. Instead, non darwinian evolution can create new genes that have never existed before.

The existence of de novo genes suggests that evolution is more creative and open-ended than NeoDarwinism traditionally allows. De novo genes may play a major role in the evolution of new species and new adaptations.

For example, a de novo gene could arise that gives an organism resistance to a new disease. This would allow the organism to survive and reproduce in the face of the disease, and it could eventually lead to the evolution of a new species.

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