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The Problem of Orphan Genes

The Problem of Orphan Genes


Genetic information is so detailed that questions often arise as to where it came from. Genes may either be homologues to genes in other species (similar in composition to genes in other organisms and assumed to have originated from a common source), or they may be entirely different. These different genes are called orphan genes. Orphan genes (often spelled ORFan genes) are species specific genes that are significantly different from all other known genes, and are thus genetically isolated from the enormous set of genetic possibilities.

Evolutionists believe that all new functional genes have evolved from earlier genes as genomes have become larger in time. It is their view that the first genome was less than a few hundred genes, such as exist in viruses today. That number evolved (they say) into a few thousand genes in bacteria and eventually these evolved to over twenty thousand in vertebrates (animals with back bones).

In harmony with this postulate, it was assumed for decades by Darwinists that all new genes have slowly evolved by gradually modifying previously existing genes in a Darwinian evolutionary fashion. One theory of gene creation is that when a gene duplicates, it may allow one copy to undergo evolution until mutations create a new function for the copy (Ohno, 1970). Thus, orthodox evolution theory taught that all genes come from other genes, and for this reason all genes will be homologues to the genes they evolved from (Guerzion and McLysaght, 2011). Specifically, it was predicted that, due to the “explosive increase in genomic data and rapid advances in molecular genetic technology, the manifold and fundamental roles of gene duplication will become even more evident and the once imaginative idea of evolution by gene duplication will be established as one of the cornerstones of evolutionary biology. This was the standard story until a few years ago.” (Zhang, 2003, p. 297). New information, especially the discovery of orphan genes, has forced a modification of that story. Other explanations for the origins of new genes besides gene duplication include “exon shuffling, retroposition, mobile elements, lateral gene transfer, gene fusion/fission, and de novo origination.” Wu et al, 2011, p. e1002379). All except the last of these explanations involve changes to existing genes.

The reason this early view of new genes has changed is largely due to the discovery of an enormous number of orphan genes that showed no evidence of evolving from preexisting genes. The gene duplication theory retains its vitality among Darwinists only because the contrary idea, namely that genes originate by spontaneous mutation, recombination and random genetic drift, has not been supported by the genetic research evidence. The problem orphan genes create for Darwinism is that the probability is miniscule that a functional gene sequence can emerge from a random sequence of the nucleic letters A, T, G, C.

As Wu et al., admit the “origin of new genes has always been an intriguing evolutionary question” (2011, p. e1002379). Some of the problems that occur when non-coding nucleotide strings are transformed into genes that specify a functional product include single genes that, although not as complex as an organ such as an eye, still require “a series of nontrivial requirements for functionality” (Siepel, 2009, p. 1693).

For example, in order for an orphan gene to encode a protein that serves a useful purpose requires “a promoter capable of initiating transcription, and presence in a region of open chromatin structure that permits transcription to occur. 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 proto-gene that was sufficiently useful for selection to take hold?” (Siepel, 2009, p. 1693). This question has forced many to rethink the question of the origin of new genes.

Siepel concluded that the origin of protein-coding genes ex-nihilo from random sequences of DNA “would seem highly improbable, almost like the elusive transmutation of lead into gold that was sought by medieval alchemists” (Siepel, 2009, p. 693). Wu et al., noted that the “de novo origin of a new protein-coding gene from non-coding DNA is considered to be a very rare occurrence in genomes” yet he has identified “60 new protein-coding genes that originated de novo on the human lineage since divergence from the chimpanzee” (Wu et al. 2011, p. e1002379). Orphan genes are now recognized to be common.

In contrast to Darwinian expectations, in order to explain orphan genes, evolutionists are forced to conclude that there exists a “growing appreciation of the oft-dismissed possibility of the evolution of new genes from scratch…” (Guerzoni and McLysaght, 2011, p. 2381). As genomic comparisons become ever more sophisticated as a result of the many major advances in sequence technology, evolutionists are forced to admit the unlikely scenario that is increasingly apparent that evolution from scratch must have often been the route to new genes throughout the history of life, and not evolution from existing genes (Doolittle, 2002, pp. 697-698). Evidence now exists that orphan genes constitute at least 30 percent or more of all genes in existing genomes (Palmieri, 2014, p. e01311). No doubt, the current rapidly progressing genetic research will uncover many more examples.

Thus, evidence now exists that a significant proportion of all functional genes did not emerge from other genes in the course of gradual evolution, but must have originated ex-nihilo (out of nothing), a finding that opposes Darwinism and supports the creation ex-nihilo view. These genes must have originated by some unknown de novo process (Wu, et al. 2011). Orphan genes are found in all life forms, from flies to humans (Palmieri, et al. 2014). Who knew that technical details could be so interesting? Indeed this issue definitely supports the creation worldview.


Doolittle, Russell. 2002. Nature, 416(6882):697–700

Guerzoni, Daniele and Aoife McLysaght. 2011. PLoS Genetics, 7(11):e1002381.

Ohno, Susumu. 1970. Evolution by Gene Duplication. New York: Springer-Verlag.

Palmieri, Nicola. et al. 2014. eLife, 3:e01311.

Siepel, Adam. 2009. Genome Research, 19(10):1693-1694.

Wu, Dong-Dong, David M. Irwin, Ya-Ping Zhang. 2011. “De Novo Origin of Human Protein-Coding Genes.” PLoS Genetics, 7(11): e1002379.

Zhang, Jianzhi. 2003. TRENDS in Ecology and Evolution, 18(6):297.

Jerry Bergman
April 2019

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