More misconceptions about junk DNA - what are we doing wrong?

I'm actively following the views of most science writers on junk DNA to see if they are keeping up on the latest results. The latest book is DNA Demystified by Alan McHughen, a molecular geneticist at the University California, Riverside. It's published by Oxford University Press, the same publisher that published John Parrington's book the deeper genome. Parrington's book was full of misleading and incorrect statements about the human genome so I was anxious to see if Oxford had upped it's game.¹, ²

You would think that any book with a title like DNA Demystified would contain the latest interpretations of DNA and genomes, especially with a subtitle like "Unraveling the double Helix." Unfortunately, the book falls far short of its objectives. I don't have time to discuss all of its shortcomings so let's just skip right to the few paragraphs that discuss junk DNA (p.46). I want to emphasize that this is not the main focus of the book. I'm selecting it because it's what I'm interested in and because I want to get a feel for how correct and accurate scientific information is, or is not, being accepted by practicing scientists. Are we falling for fake news?

When it was first discovered, the nongenic DNA was sometimes called—somewhat derisively by people who didn't know better—"junk DNA" because it had no obvious utility, and they foolishly assumed that if it wasn't carrying coding information it must be useless trash.

In evolutionary terms, a DNA sequence with no function is simply dead weight that gets carried along, at some cost to the organism, to be jettisoned at the first opportunity. If the sequences were not adaptively important, evolution would have kicked them out as expendable excess baggage. The fact that nonrecipe DNA continues to be part of the human and other eukaryotic genomes over millions of years indicates that there is some adaptive value to carrying the "junk baggage" along, even if that value remains unclear to us today.

In addition to various putative regulatory and structural functions, recent evidence indicates that mutations in the integernic noncoding DNA leads to a increase in susceptibility to various diseases. If confirmed, it would show a clear adaptive value to "junk" DNA.

Today, we appreciate that this is not useless junk and now call it noncoding DNA. About 80% of the DNA is known to have some activity, even if the exact activity hasn't been determined. We now usually call it the more benign dark DNA.

OMG! It looks like the proponents of junk DNA have failed to make an impression on this author.

There's a lot of misinformation in those few paragraphs, as most Sandwalk readers know. Here are a few highlights ...

• Nongenic DNA was never called junk DNA by any knowledgeable scientist back in the 1970s or at any time since. That's misleading information that has been debunked so many times that it astounds me how any modern molecular geneticist could possibly believe it [Stop Using the Term "Noncoding DNA:" It Doesn't Mean What You Think It Means]. Some of the "foolish" scientists who taught us about junk DNA include Susumu Ohno, Sydney Brenner, Motoo Kimura, Francis Crick, Thomas Jukes, and Ford Doolittle. Apparently they didn't know any better. The list of modern "fools" is even longer and it contains the names of dozens of highly respected scientists who are experts on genomes and molecular evolution. I do not understand how any modern scientist could dismiss the work of experts in the field of genomics by imagining that they were/are stupid enough to dismiss all noncoding DNA as junk. How did that silly myth ever take hold?
• The author has a 1950's adaptationist view of evolution. He is unaware of the fact that modern evolutionary theory can easily accommodate genomes that are 90% junk. He is also unaware of the data since there's good experimental evidence to support the idea that less than 10% of the sequences in our genome are under selective constraint
Five Things You Should Know if You Want to Participate in the Junk DNA Debate
• We have known for decades that regulatory sequences are abundant and essential. They were NEVER dismissed as junk DNA. The fact that mutations in regulatory regions might cause diseases in humans is perfectly consistent with everything we known about functional DNA and it has nothing to do with junk. (I should also note that mutations in real junk DNA can cause diseases but that doesn't mean the DNA isn't junk.)
• Once again, there was never a time when knowledgeable scientists were confused about the difference between junk DNA and noncoding DNA. A substantial percentage of noncoding DNA is junk but the most of the functions residing in noncoding DNA have been known for fifty years [What's In Your Genome? - The Pie Chart]. The idea that 80% of our genome has some sort of functional biological activity has been thoroughly debunked and discredited. Knowledgeable scientists do NOT refer to most of our genome as "dark" DNA because they are fully aware of all the positive evidence showing that most of it (~90%) is junk. It's disappointing that the majority of scientists are unaware of this evidence [Required reading for the junk DNA debate]

Let's be clear about one thing. The propagation of this misleading information about junk DNA is not entirely Alan McHughen's fault. He is merely repeating what he thinks is the consensus view of the experts—it is not his field. I might criticize him for not doing his homework before publishing this in his book but I assume that he had no idea that what he was writing was controversial.

The fault lies with those of us who are proponents of junk DNA and with science culture. Somehow, the idea that 90% of our genome is junk has failed to make an impression on our fellow scientists. Somehow, the idea that evolution includes Neutral Theory, random genetic drift, and a thorough understanding of the principles of population genetics has failed to reach the average biologist. What are we doing wrong? How can we fix it?

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1. Full disclosure, Oxford declined to publish my book after I sent them a proposal.

2. Read my posts on Parrington's book at: John Parrington discusses genome sequence conservation.