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A Reader Asks, "Are De Novo Genes Real?"


We get good questions here at Evolution News. (Give us yours by hitting the orange Email Us button at the top of the page.) Today, a reader writes to ask, "Are de novo genes real?" This is a question that touches on a number of topics relevant to evolutionary biology, dealing with one of the most exciting aspects of genomic research today. So what are these things called de novo genes?

De novo genes are genes that are present in a particular species or taxonomic group, and not present in any others. Why are they there and where did they come from? To answer these questions we have to first deal with some important assumptions of evolutionary biology.

The first assumption is that sibling species are the product of descent with modification. The evidence cited in favor of this idea is that there is similarity of DNA sequence between sibling species, and that organisms can be grouped in nested hierarchies based on sequence comparisons. Now this hypothesis of common descent may be right. However, there are unresolved contradictions in the literature. So common descent is not unequivocally proven. De novo genes are one of those challenges to common descent. Let me explain why.

De novo genes, new genes present in one taxonomic group but not in others, are sometimes called orphan genes because they have no parent genes. They are also called taxonomically restricted genes (TRGs), because they may be shared by closely related species of the same taxon, but not others. What's a taxon? It's a level of classification, such as species, genus, family, order, class or phylum. Species of the same genus, for example, may share genes in common that are missing from all other species.

Because the field of research is still developing, different research groups use different criteria for deciding what counts as a TRG. For example, one recent estimate says that there are 634 genes that appear to have arisen de novo in the human genome, as compared with the chimpanzee and macaque genomes. But they counted RNA transcripts as genes, even if they have not yet been shown to code for protein. Another older estimate of over a thousand transcripts was finally reduced to a much lower number of de novo genes, because the researchers ruled out almost all of those candidate genes as non-protein coding. For a discussion about why this is, go here.

Despite these disagreements, de novo genes do exist. But when their origin -- where they came from -- is discussed, it reveals yet another assumption of evolutionary biologists. Evolutionists say, "Look, these orphan genes arose de novo. We can see how they might have been spliced together from similar DNA present elsewhere in the genome, or they might have come from non-coding DNA that has acquired a promoter or transcription factor binding site, and so is now expressed, and makes a functional protein, in the right place and at the right time."

These sentences reveal the second assumption -- that the existence of these new genes indicates there are natural processes to make them. After all, it must be possible to splice or activate new sequences to make TRGs, because there are TRGs.

That's an assumption of naturalism. The problem is there is no evidence to show that those proposed mechanisms actually work. There are no experiments that I know of to demonstrate that splicing yields functional products. Attempts in the lab show that splicing together even related protein domains yields non-functional products. Also, no one has shown that it is easy to acquire a promoter or transcription factor binding site so as to turn inactive, non-coding DNA into expressed, functional DNA. Getting a functional protein from random non-coding sequence is impossibly hard and would have to be demonstrated. If the function is regulating other genes via RNA, that would have to be proven to be feasible, too.

So do we know where TRGs came from? If no one tests how hard it is to splice together random sequence and get functional stuff, or how hard it is to acquire a new promoter, then we don't know whether de novo genes can be developed by evolutionary processes. If not, the alternative is shocking to evolutionary biologists -- perhaps, just perhaps they were made by a designer for that particular species or group. Perhaps the non-coding DNA was already ready to be functional, like an actor waiting in the wings for his cue, and was only activated in that one particular taxonomic group.

Bear in mind that TRGs can be up to 10-20 percent of a taxonomic group's genome, and may encode many of the special proteins unique to that taxonomic group. That's a huge chunk of DNA to arise by natural processes alone, and a big challenge for common descent. I am thinking of the phylum Cnidaria here. All Cnidaria (sea anemones, jelly fish, and Hydra for example) have tentacles with specialized cells called cnidocytes or nematocysts, which eject a little barbed tubule with a toxin into whatever touches them. They use these cells to capture and immobilize their prey. Many of the specialized proteins needed to make the nematocysts are TRGs specific to the phylum Cnidaria. Cnidaria are among the oldest of all extant phyla. Was their origin unique?

Take home lesson: Are de novo genes real? Yes. Do we know where they came from? No. Do they say something important about evolutionary processes? Indeed. But what they say remains to be seen.

Image: Pacific sea nettles, via Wikicommons.