What makes us human? Some would say it’s our genes. I don’t want to argue the case that we are more than our genes, though we are. I simply want to point out that interesting new research indicates we have a number of new genes — genes that are specifically human — in our genome.
These new genes are few in number, some would say, but there is a current bias in genome annotation against classifying sequences as novel genes. Estimates range from three to sixty to three hundred human-specific protein-coding genes. In fact, one genetic analysis came up with 1177 human-specific genes, and then proceeded to systematically eliminate all of them as non-coding for a variety of reasons, reasons that may or may not be valid. Why does this matter? Because 1177 genes is nearly 6 percent of our genome, and 300 is about 1.5 percent. Those numbers are not something to trifle with, given that our reported base-pair difference with chimps is about 1.3 percent.
Some researchers argue that the discrepancy in number is due to pruning of the data. Identifying these novel genes relies heavily on computer analysis of the human genome, and depends entirely on the assumptions made and methods used by the researchers. Some of it may be due to the same kind of bias we saw with ENCODE, the unwillingness to ascribe function to transcriptionally active non-coding DNA. Some of it may be due to reluctance to admit there are so many de novo genes, and a wish to ascribe them to junk. Some of it is definitely due to the way a gene is defined. The databases now annotate DNA as a gene if it has a homologous sequence (a sequence also present in another organism), which is precisely what novel genes do not have. One group described the problem thus:
A serious limitation in this approach is that it relies on existing gene lists that have been annotated using criteria that usually include the presence of a homolog in other genomes. Novel genes fail to meet this criterion by definition, thus they are usually not reliably annotated. Wu et al.‘s study  highlights the volatility of the annotation of putatively novel genes — over half of the candidate de novo genes they identified are not included in the more recent Ensembl gene lists they used (version 56), and by version 60 only six of these genes were still listed.
How important are these new genes? Some are associated with human disease, indicating their functional importance. Many of them may be used to regulate the expression of other genes. In fact, many of these genes are expressed in the developing human brain, specifically the neo-cortex, where rational thought comes from. Many may also function in the testes. (Don’t ask me why. There appear to be a large number of new genes in other species’ testes too).
In other organisms, similar stretches of DNA are non-functional, whereas in our genomes they are transcribed and, in many cases, translated into protein. They lack similarity in sequence to other coding genes anywhere in the catalog of all known protein-coding genes. Because they have no relatives in other genomes, they are called orphan genes. As such, they present a strong challenge to the Darwinian story. This is because in Darwinian terms, repurposing genes requires gaining some means of turning on transcription and translation and acquiring a useful function.
In fact, until about ten years ago, everyone thought that evolving a new gene would be difficult if not impossible. Yet now we see new genes in every new genome that is sequenced, representing on average about 10 percent of that genome. Many of these orphan genes play important roles in their respective organisms. Indeed, as I said before, many of our new genes are involved in the developing fetal brain, in the neo-cortex, the part of us that distinguishes us most clearly from chimps.
It’s not something borrowed from other organisms, it’s something new that may contribute to making us who we are.