Genes hold information that is used to construct protein and RNA molecules which do various tasks in the cell. A gene is copied in a process known as transcription. In the case of a protein-coding gene the transcript is edited and converted into a protein in a process known as translation. All of this is guided by elaborate regulatory processes that occur before, during and after this sequence of transcription, editing and translation.
For instance, some of our DNA which was thought to be of little use actually has a key regulatory role. This DNA is transcribed into strands of about 20 nucleotides, known as microRNA. These short snippets bind and interfere with RNA transcripts—copies of DNA genes—when the production of the gene needs to be slowed.
MicroRNAs can also help to modify the translation process by stimulating programmed ribosomal frameshifting. Two microRNAs attach to the RNA transcript resulting in a pseudoknot, or triplex, RNA structure form which causes the reading frameshift to occur. (Belew)
MicroRNAs do not only come from a cell’s DNA. MicroRNAs can also be imported from nearby cells, thus allowing cells to communicate and influence each other. This helps to explain how cells can differentiate in a growing embryo according to their position within the embryo. (Carlsbecker)
MicroRNAs can also come from the food we eat. In other words, food not only contains carbohydrates, proteins, fat, minerals, vitamins and so forth, it also contains information—in the form of these regulatory snippets of microRNA—which regulate our gene production. (Zhang)
While microRNAs regulate the production of proteins, the microRNAs themselves also need to be regulated. So there is a network of proteins that tightly control microRNA production as well as their removal. “Just the sheer existence of these exotic regulators,” explained one scientist, “suggests that our understanding about the most basic things—such as how a cell turns on and off—is incredibly naïve.” (Hayden)
Two basic predictions that evolutionary theory makes regarding microRNAs are that (i) like all of biology, they arose gradually via randomly occurring biological variation (such as mutations) and (ii) as a consequence of this evolutionary origin, microRNAs should approximately form evolution’s common descent pattern. Today’s science has falsified both of these predictions.
MicroRNAs are unlikely to have gradually evolved via random mutations, for too many mutations are required. Without the prior existence of genes and the protein synthesis process microRNAs would be useless. And without the prior existence of their regulatory processes, microRNAs would wreak havoc.
Given the failure of the first prediction, it is not surprising that the second prediction has also failed. The microRNA genetic sequences do not fall into the expected common descent pattern. That is, when compared across different species, microRNAs do not align with the evolutionary tree. As one scientist explained, “I've looked at thousands of microRNA genes and I can't find a single example that would support the traditional [evolutionary] tree.” (Dolgin)
While there remain questions about these new phylogenetic data, “What we know at this stage,” explained another evolutionist, “is that we do have a very serious incongruence.” In other words, different types of data report very different evolutionary trees. The conflict is much greater than normal statistical variations.
“There have to be,” added another evolutionist, “other explanations.” One explanation is that microRNAs evolve in some unexpected way. Another is that the traditional evolutionary tree is all wrong. Or evolutionists may consider other explanations. But in any case, microRNAs are yet another example of evidence that does not fit evolutionary expectations. Once again, the theory will need to be modified in complex ways to fit the new findings.
In the meantime, scientists are finding that imposing the common descent pattern, where microRNAs must be conserved across species, is hampering scientific research:
These results highlight the limitations that can result from imposing the requirement that miRNAs be conserved across organisms. Such requirements will in turn result in our missing bona fide organism-specific miRNAs and could perhaps explain why many of these novel miRNAs have not been previously identified. (Londin)
Evolutionary theory has been limiting the science. While the common descent pattern has been the guide since the initial microRNA studies, these researchers “liberated” themselves from that constraint, and this is leading to good scientific progress:
In the early days of the miRNA field, there was an emphasis on identifying miRNAs that are conserved across organisms … Nonetheless, species-specific miRNAs have also been described and characterized as have been miRNAs that are present only in one or a few species of the same genus. Therefore, enforcing an organism-conservation requirement during miRNA searches is bound to limit the number of potential miRNAs that can be discovered, leaving organism- and lineage-specific miRNAs undiscovered. In our effort to further characterize the human miRNA repertoire, we liberated ourselves from the conservation requirement … These findings strongly suggest the possibility of a wide-ranging species-specific miRNA-ome that has yet to be characterized. (Londin)
The two microRNA predictions have been falsified and, not surprisingly, the evolutionary assumption has hampered the scientific research of how microRNAs work.
Belew, Ashton T., et. al. 2014. “Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway.” Nature 512:265-9.
Carlsbecker, Annelie, et. al. 2010. “Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate.” Nature 465:316-21.
Dolgin, Elie. 2012. “Phylogeny: Rewriting evolution.” Nature 486:460-2.
Hayden, Erika Check. 2010. “Human genome at ten: Life is complicated.” Nature 464:664-7.
Londin, Eric, et. al. 2015. “Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs.” Proc Natl Acad Sci USA 112:E1106-15.

Zhang, L., et. al. 2012. “Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA.” Cell Research 22:107-26.