Darwinian Alchemy of new (denovo) Genes- "Just imagine!"


Article: Darwinian alchemy: Human genes from noncoding DNA

"De novo gene origins raise the question of how evolution by natural selection can produce functional genes from noncoding DNA.

How could all of these pieces fall into place through the random processes of mutation, recombination, and neutral drift—or at least enough of these pieces to produce a protogene that was sufficiently useful for selection to take hold?

One can imagine a process by which short, simple genes periodically arise de novo, then gradually become more complex over time."

The discovery that human genes can arise de novo from noncoding DNA challenges neo darwinism. Neo darwinism suggests that evolution is simply a process of natural selection acting on existing genes. This does not explain the process of creating new genes from scratch. The discovery of de novo gene origins suggests that evolution is not simply a process of adaptation, but also a process of exaptation, or the co-option of existing genes for new purposes. The discovery of de novo gene origins suggests that evolution is not simply a process of chance variation, but also a process of constraint, or the limitation of possible evolutionary changes by the existing gene pool. This challenges the neo darwinian view that evolution is a process of random variation.

The conventional wisdom has been that, in the emergence of novel genes, “natural selection merely modified, while redundancy created.” In other words, new genes generally arise by the duplication of existing genes, a NonDarwinian process.

However, in recent years, there have been several reports of de novo gene origins in Drosophila and yeast. And now, in a new study, Knowles and McLysaght (2009) have identified three human genes that have no known homologs in any other genome.

Validating alleged gene births is a tricky business, because it requires showing not only that the new genes are functional but also that their evolutionary antecedents were nonfunctional. Knowles and McLysaght have done this by using a variety of methods, including phylogenetic analysis, comparative genomics, and cDNA cloning.

Their results strongly suggest that the three genes are transcribed and translated in humans, yet did not encode proteins (noncoding DNA) in ancestral primates. As is typical of “orphan” genes, little is known about their functions. Again NeoDarwinism only acts on coding genes.

The discovery of de novo gene origins raises the question of how evolution by natural selection can produce functional genes from noncoding DNA. By definition NeoDarwinism only works on coding DNA. One possibility is that evolution arrives at new forms by “tinkering” with forms that have previously evolved for other purposes. "Tinkering" is a nebulous concept excusing a lack of explanation by NeoDarwinism. Tinkerbell did it!

Another possibility is that new genes can arise by recombining existing genetic elements in new ways. For example, a new gene could be created by combining a promoter from one gene with the coding sequence from another gene. Promoter regions are typically CpG islands. These repetitive dinucleotides are noncoding DNA and are not under natural selection.

Finally, it is also possible that new genes can arise by chance mutations in noncoding DNA. However NeoDarwinism does not fix mutations in noncoding DNA by definition as they are not under natural selection. These mutations could create new ORFs, or they could alter the expression of existing genes.

Regardless (iow we don't have a clue) of how they arise, de novo gene origins are important because they provide a new source of genetic variation. This variation can be fuel for natural selection, and it can also lead to the emergence of new traits and functions. A perfect argument from ignorance. We don't know how therefore "Darwin did it." 

Implications of de novo gene origins for human evolution

The discovery of de novo gene origins in humans has several implications for our understanding of human evolution. First, it suggests that the human genome is more fluid and dynamic than previously thought. Second, it implies that new genes can arise quickly, on the order of millions of years. Third, it raises the possibility that de novo gene origins may have played a significant role in the evolution of human-specific traits.

For example, one of the genes identified by Knowles and McLysaght is expressed in the brain and is thought to be involved in cognitive function. It is possible that this gene arose de novo in humans, and that it contributed to the development of our unique cognitive abilities.

Future directions

The study by Knowles and McLysaght is just the beginning of our understanding of de novo gene origins in humans. More research is needed to identify additional de novo genes, to characterize their functions, and to understand the molecular mechanisms by which they arise.

Overall, the discovery of de novo gene origins is an exciting development in the field of evolutionary biology. It provides us with a new way to think about the evolution of the human genome and the origins of human-specific traits. 

They summarize:

"One can imagine a process by which short, simple genes periodically arise de novo, then gradually become more complex over time."

All you have to do is imagine Darwinian Alchemy and use "specific" mechanisms like alchemy, fuel, tinker and Darwin did it.  How can you go wrong!?

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