Junk DNA: So much wrong in so few words

[T_aquaticus]

Inspired by my favorite molecular biology crumudgeon Larry Moran, how many false claims about junk DNA and molecular biology can we find in this abstract?

For decades, the miniscule protein-coding portion of the genome was the primary focus of medical research. The sequencing of the human genome showed that only ∼2% of our genes ultimately code for proteins, and many in the scientific community believed that the remaining 98% was simply non-functional “junk” (Mattick and Makunin, 2006; Slack, 2006). However, the ENCODE project revealed that the non-protein coding portion of the genome is copied into thousands of RNA molecules (Djebali et al., 2012; Gerstein et al., 2012) that not only regulate fundamental biological processes such as growth, development, and organ function, but also appear to play a critical role in the whole spectrum of human disease, notably cancer (for recent reviews, see Adams et al., 2017; Deveson et al., 2017; Rupaimoole and Slack, 2017).

Slack, F.J. and Chinnaiyan, A.M. (2019) The Role of Non-coding RNAs in Oncology. Cell 179:1033-1055

I will start with the easiest one.

1. Few, if any, scientists from the last 50 years thought that the only functional DNA in the human genome were exons in protein coding genes.

[Robert]

2. It probably should be 2% of the genome, not of the genes - I’m not 100% on board with the reductionist definition of a gene, but it’s the one in common use. (On the other hand that’s not a claim about junk DNA.)
3. There are indeed thousands of functional RNA molecules (in addition to mRNAs), but those thousands are still only a minuscule fraction of the genome - equivocation between some of the non-protein coding portion of the genome and all of it.

[Roy (34-year veteran)]

It’s only been 16 years since we completed sequencing of the human genome and found out which bits were and which bits were not non-coding - so we can’t have been focusing on the coding portions for decades. Nor was it really the primary focus during that time, either.

[Robert]

We may not have yet pinned down the coding portion of the genome. There have been changes in which segments are thought to code for proteins (with a general downward trend); if I have the right impression the process of analysing the genome for functional ORFs still isn’t finished.

[T_aquaticus]

@Roy

It’s only been 16 years since we completed sequencing of the human genome and found out which bits were and which bits were not non-coding - so we can’t have been focusing on the coding portions for decades .

We had a pretty good grasp of what percentage of the human genome is devoted to genes for a while.

Even if an allowance is made for the existence in multiplicates of certain genes, it is still concluded that, at most, only 6% of our DNA base sequences is utilized as genes.
Ohno, S. (1972) So much “junk” in our genome. In H. H. Smith (Ed.), Evolution of genetic systems (Vol. 23, pp. 366-370): Brookhaven symposia in biology.

[John_Harshman]

I’ll play.

2. Most of our genes code for proteins; the 2% claim assumes that the entire genome consists of genes.

3. “Non-coding” is not, never has been, assumed to by synonymous with “junk”.

4. ENCODE. Insert Nelson Muntz style “Ha-ha”. Similar response to any citation containing the name “Mattick”.

5. Assumes that if one non-coding RNA is functional, they all are, no matter how rarely transcribed.

6. Assumes that a sequence associated with cancer must be functional in a normal cell.