Popular press wildly overblows “gene for humanity”

I’m about to describe one of the worst examples of science journalism I’ve seen in ages. It is a lesson on how the popular press overblows interesting scientific findings into world-shaking discoveries.

miRNAs, or “microRNAs”, are small molecules of RNA, produced by the DNA, that have recently been discovered to play an important role in gene regulation, usually by binding to a “regulatory portion” of a gene and silencing that gene (i.e., preventing its expression).

A new paper in Nature Communications by Hai Yang Hu and others (some of them from the University of Edinburgh) report a new miRNA that is specific to the human lineage: it’s not present in our closest relative, chimpanzees, or in 10 other species. By looking for miRNAs specific to humans, their clear hope was to find genes important in “humanness”: those traits that set us off from other species.

And indeed they did find one, which is what their report is about. But the popular press has distorted this finding to an unbelievable length, claiming that this is THE gene responsible for “humanity,” the one moiety of DNA that is what makes us human.

First, what did Hu et al. find? Here’s the abstract of their paper:

MicroRNA-mediated gene regulation is important in many physiological processes. Here we explore the roles of a microRNA, miR-941, in human evolution. We find that miR-941 emerged de novo in the human lineage, between six and one million years ago, from an evolutionarily volatile tandem repeat sequence. Its copy-number remains polymorphic in humans and shows a trend for decreasing copy-number with migration out of Africa. Emergence of miR-941 was accompanied by accelerated loss of miR-941-binding sites, presumably to escape regulation. We further show that miR-941 is highly expressed in pluripotent cells, repressed upon differentiation and preferentially targets genes in hedgehog- and insulin-signalling pathways, thus suggesting roles in cellular differentiation. Human-specific effects of miR-941 regulation are detectable in the brain and affect genes involved in neurotransmitter signalling. Taken together, these results implicate miR-941 in human evolution, and provide an example of rapid regulatory evolution in the human linage.

So the facts are that this miRNA, miR-941, is not found in our closest relatives, but emerged in our genome between 6 and 1 million years ago—the period of human evolution. It is highly expressed in our brain compared to other miRNAs.  Other analyses show that the early Denisovans had the gene, and modern human populations vary in copy number, with individuals having between 2 and 11 copies.  Finally, the number of potential binding sites of this regulatory molecule has decreased in humans, which the authors suspect means that some of the binding sites that remain are important in humans (but not other species’) gene regulation. There’s one more interesting observation. As the authors note:

Another hint for the potential involvement of miR-941 and its host gene in neuronal functions comes from studies of a microdeletion in chr20 q13.33 chromosomal region containing pre-miR-941. Individuals containing this microdeletion display mental retardation, developmental delay, as well as speech and language defects.

True, but as the authors note, that “microdeleted region” contains a lot more genes than just miR-941:

Besides the pre-miR-941 cluster, the deleted region usually contains more than 20 protein-coding genes. Still, it remains possible that miR-941 might be responsible for or contribute to the disease phenotype.

“Remains possible”! Indeed, but it also remains possible that deletetion of any of the other 20-odd genes, or a combination of them, could also cause the syndrome. Indeed, I suspect that since the effects of the deletion include developmental delay and speech defects, more than one gene might be responsible.  DNA sequencing of this region, and comparison to the sequences of chimps, would be most enlightening here.

The upshot: we have a human-specific molecule, miR-941, that regulates gene expression in our brains, and some of the genes it might have regulated have dropped out of the pathway. What does that mean?  We don’t really know. We don’t know what the miRNA does; only that it does something in the human brain that it doesn’t do in the brains of other mammals. And when the region containing it and many other genes is deleted, we get humans with mental retardation, developmental problems, and speech defects. The authors engage in some speculation about the importance of this gene in human evolution, but are very careful to hedge their conclusions:

In conclusion, we show that the emergence and rapid expansion of miR-941 precursor sequence took place in the human evolutionary lineage between six and one million years ago, and was accompanied by an exceptional increase in miR-941 expression level. The emergence of miR-941 was accompanied by accelerated loss of its binding sites, presumably due to deleterious effects of miR-941-guided regulation. Functionally, miR-941 could be associated with hedgehog- and insulin-signaling pathways, and thus potentially has a role in the evolution of human longevity. Furthermore, human-specific effects of miR-941 regulation are detectable in the human brain and affect genes involved in neurotransmitter signaling. Deletion of the genomic region containing pre-miR-941 results in disruption of human-specific cognitive functions including language and speech. Taken together, the unusual features of miR-941 evolution, as well as its potential association with functions linked to human longevity and cognition, suggest roles of miR-941 in the evolution of human-specific phenotypes.

Note: their results “suggest roles of miR-941 in the evolution of human-specific phenotypes.”

So what does the “popular press” do with this finding? They conclude that miR-941 is THE ONE GENE that makes us human, and differentiates us from the other apes. In a breathless piece called, erroneously, “Scientists reveal single gene is the difference between humans and apes,” (there are of course many genetic differences between humans and other apes), the website Medical Daily claims that this is the Gene For Humanity. The Medical Daily report:

Now, researchers believe that they have found the definitive difference between humans and other primates, and they think that the difference all comes down to a single gene.

Researchers from the University of Edinburgh in Scotland [JAC note: and other places, like China, which is where Hu works!] attribute the split of humanity from apes to the gene miR-941. They say that the gene played an integral role in human development and contributed to humans’ ability to use tools and learn languages.. .

Hu et al. do nothing of the sort. Read their paper (free at the link below)! Medical Daily continues with its litany of exaggeration and errors:

Humans share 96 percent of their genes with other primates. Of the 4 percent that humans alone have, a significant portion of it has been widely labeled “junk DNA”. Researchers have since [said] that “junk DNA” is functional, even though it does not code. This is the first time that a gene that humans and other primates do not share has been shown to actually have a specific function within the body.

First of all, not all “junk” DNA is functional. Larry Moran has written extensively about this on Sandwalk (e.g., here and here.) There is no basis for implying that all, or even most, junk DNA actually does something.

The claim that this is the first novel human gene that has a specific function may well be right (that conclusion is above my pay grade), since miR-941 does appear to regulate the insulin and “hedgehog” (a gene involved in development) pathway, but it may have many other functions that we don’t know.  And there are other genes that are unique to humans and not other apes; we just don’t know their function yet.  Those, too, can be “humanness” genes. I suspect, in the end, there will be dozens to hundreds of genes that explain our differences from other apes: genes involved in bipedality, loss of hair, delayed infant development, cognition, and so on. But that’s not what Medical Daily wants it readers to think: there must have been one gene:

The gene is highly active in the regions of the brain that control language learning and decision making, indicating that it may play a significant role in the higher brain functions that make humans, well, human.

It’s hard for me to believe that cognition and language all come down to the evolution of a single miRNA, and, indeed, the authors never make such a suggestion. That would imply that cognition and language arose relatively suddenly, during the period when the new miRNA arose and became “fixed” (i.e. spread to all humans).  Yet our increase in brain size took place over several million years and, I think, our mental capacity increased apace.

This is an appallingly bad example of science journalism. It’s not the fault of the authors, who are careful with their suggstions. It’s the fault of Medical Daily, which wanted to make a big splash. Shame on them. In the end, miR-941 may play a role in the difference in cognition and speech between chimps and humans. But I’d bet thousands of dollars that it doesn’t play a huge role in that difference.

This all reminds me of the gene FOXP2, once also touted as the “humanness” gene because it evolved rapidly in the human lineage and mutations in the gene affect language ability.  That gene, too, hasn’t panned out as a critical factor in the evolution of “humanness.”  We differ from our closest relatives in many, many genes, and singling out one of them as a “humanness” gene is, and will always be, a mug’s game.
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Hu, H. Y. et al. 2012. Evolution of the human0-specific microRNA miR941. Nature Communications 3, Article number: 1145 doi:10.1038/ncomms2146