Orphan Genes

Scientists started comparing whole genome sequences of various species in the 1990’s. Genes that are only found in one or very closely related species are called unique, de novo, ORFan or orphan genes. The amazing thing is that the more they compare species, the more unique genes they find. These genes make up about 10-20% of each organism’s whole set, percentages given by Dr. Ann Gauger, "Orphan Genes: A Guide for the Perplexed," Evolution News, July 30, 2013. I have seen research even in the 30% range. These unique genes are so different from each other that the chance they could have come from an evolutionary sequence is vanishingly small. This is, for one reason, because there could have been no more than 10^50 organisms on Earth so far even if the Earth is very old. The unique genes are statistically so far apart that even this many organisms are not enough to sort through the various possibilities.  (And only one in about 10^70 proteins is functional. So the sorting of proteins for functional ones makes evolution by chance look pretty much impossible.) In contrast, if all genes (and corresponding proteins) were closely related and in obvious sequence in species, Darwin would have been proven right.

Eugene Koonin is Senior Investigator of comparative genomics at National Center for Biotechnology Information (NCBI, a division of NIH) and has written many articles. So he is on the front lines of comparative genomics. He and Yuri Wolf wrote an article in 2008: Koonin and Wolf,  "Genomics of bacteria and archaea: emerging dynamic view of the prokaryotic world," Nucleic Acids Research 36, 21 (Dec. 1 2008): 6688-6719. They found there were some proteins common to many species of bacteria and archaea (one-celled organisms different from bacteria). But what surprised them was the vast amount of variety between species and the unique genes. Koonin has become part of a movement to find other explanations for evolution instead of neo-Darwinism called the Third Way of Evolution. The "evolution" part is because Koonin is committed to evolution although his move shows that he believes neo-Darwinian evolution is falsified. But these findings of comparative genomics also support direct creation of species.

Another article by J. Muller, et al., "eggNOG v2.0," Nucleic Acids Research, Database Issue 38 (Jan. 2010): D190-D195, compares various species. In the diagram there are species names in the middle with radiating lines that go out to colors of the graph. The green and orange represent genes which are related, but the outer gray areas are orphan genes which do not match other species (much easier to see in the full article at the title link).

A more recent article by Jorge Ruiz-Orera, et al., "Origins of de novo genes in human and chimpanzee," PLOS Genetics, Dec. 1, 2015, has reinforced these findings. The researcher and his group were looking for unique human and chimpanzee genes and found them. Their author summary starts:

For the past 20 years scientists have puzzled over a strange-yet-ubiquitous genomic phenomenon; in every genome there are sets of genes which are unique to that particular species i.e. lacking homologues in any other species.

Homologues are related genes. As stated above, these unique genes cannot be explained by the supposed machines of evolution: mutation and selection. The complete published paper can be found at the title link.

On a related subject, a problem in the past was that in comparing genes, scientists used genes they already had to see if they were in the other organisms. This left sequences that did not match out of the loop of potential genes. However, they have begun to use other criteria, such as start and stop sequences, to now identify more non-matching areas that look like genes. This is promising to show even more unique genes.