I've been complaining for years about how opponents of junk DNA misrepresent and distort the scientific literature. The same complaints apply to the misrepresentation of data on alternative splicing and on the prevalence of noncoding genes. Sometimes the misrepresentation is subtle so you hardly notice it.

I'm going to illustrate subtle misrepresentation by quoting a recent commentary on Lncrnas that's just been published in BioEssays. The main part of the essay deals with ways of determining the function of lncRNAs with an emphasis on the sructures of RNA and RNA-protein complexes. The authors don't make any specific claims about the number of functional RNAs in humans but it's clear from the context that they think this number is very large.

Graf, J. and Kretz, M. (2020) From structure to function: Route to understanding lncRNA mechanism. BioEssays [doi: https://doi.org/10.1002/bies.202000027]

With fundamental cellular functions ranging from energy metabolism to structural components, over signal transduction to being key regulators of gene expression, proteins were attributed great scientific attention, while—with a few exceptions—the RNA was contemplated as the inevitable intermediary required for protein production. However, this picture changed dramatically when high‐throughput sequencing data revealed that more than two‐thirds of the human genome are actively transcribed into RNA but only

There's nothing in that paragraph that's false but the net effect is very misleading. The best way to illustrate this is for me to re-write the paragraph from the point of view of a skeptic. My version (below) contains no false information but the perspective is very different. I'm pretty sure that opponents of junk DNA would see my version as a misrepresentation.

Humans cells contain many examples of well-characterized noncoding RNAs that we've known about for many decades. These include transfer RNAs, ribosomal RNAs,and several classes of small RNAs such as snoRNAs, snRNAs, micro RNAs, siRNAs, and piwiRNAs. In addition, there are a number of unique noncodng RNAs that are found in many species such as the RNA component of RNAseP and the 7SL RNA of signal transduction particles. There are also many larger noncoding RNAs that are generally grouped together as long-noncoding RNAs or lncRNAs. The function of some of these lncRNAs is well known—examples include Xist and HOTAIR—but many of these transcripts have not been associated with any known function.

We have known for more than half a century that most of the human genome is transcribed but the extent of pervasive transcription has only become clear since the 1990s. Most of the transcripts are not conserved and they are rapidly degraded so that they are usually present at less than one copy per cell. This has led to the widespread belief that these transcripts are nonfunctional junk RNA produced by spurious transcription. However, it seems likely that some of these RNAs will prove to have a function. One way to identify these candidates is to look at the secondary and tertiary structures of long transcripts and their interaction with identifiable proteins.

I believe that the proper way to write about these transcripts is to emphasize that they are mostly junk. That doesn't preclude looking for function in a small subset where there's evidence for function but it's a very different perspective from the one usually taken in these papers. The usual approach is to emphasize the exciting new discovery of lncRNAs making it seem like they all have some mysterious function waiting to be revealed.¹

• How many lncRNAs are functional?
• John Mattick still claims that most lncRNAs are functional
• How many lncRNAs are functional: can sequence comparisons tell us the answer?
• More stupid hype about lncRNAs

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1. It goes without saying that lots of research grant funding will be required to reveal the mysterious functions.