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Thursday, July 28, 2022

Kat Arney defends junk DNA

I'm a big fan of Kat Arney and I loved her 2016 book Herding Hemingway's Cats where she interviews a number of prominent scientists. If you haven't read it you should try and get a copy even if it's just to read the chapters on Mark Ptashne, Dan Graur, and Adrian Bird. The last chapter begins with an attempt to interview Evelyn Fox Keller but don't be put off by that because the rest of the chapter is very scientific.

Kar Arney gets mentioned a couple of times in my book and I quote her opinion of epigenetics from the chapter on Adrian Bird. She has a much better understanding of genes, genomes, and junk DNA that every other person who's ever written a book on those subjects. I especially like what she has to say about her journey of discovery on page 259 near the end of the book.

Things that I thought were solid fact have been exposed as dogma and scientific hearsay, based on little evidence but repeated enough times by researchers, textbooks, and journalists until they feel real.
                                                                                Kat Arney (2016)

Kat Arney has just (July 28, 2022) posted a Genetics Society podcast on Genetics Unzipped. The main title is Does size matter when it comes to your genes and the subsections are "Where have all the genes gone?" "Genes or junk?" and "Are you more special than an onion?" You can listen to the podcast on that site (24 minutes) or read the entire transcript.

I don't entirely agree with everything she says in the podcast but she should be applauded for defending junk DNA in the face of all the scientific hearsay that out there. Good for her.

Here's three things that I might have said differently.

  • I don't agree with her historical account of estimates of the number of genes in the human genome [False History and the Number of Genes 2010]. The knowledgeable experts in the field were predicting about 30,000 genes and their estimates weren't far off. The figure below is from Hatje et al. (2019). Note the anomalous estimates from the GeneSweep lottery and the EST data. The EST data were known to be highly suspect. This is important because the false narrative promotes the idea that scientists knew very little about the human genome before the sequence was published and it promotes the idea that there's some great mystery (too few genes) that needs to be solved.
  • I disagree with her statement that "actual genes makes up less than 2% of all the DNA in the whole human genome." My disagreement depends somewhat on the definition of a gene but that's not really controversial. We're talking about the molecular gene and that's defined as "A gene is a DNA sequence that is transcribed to produce a functional product" [What Is a Gene?]. There are exceptions but this is the best definition we have. The fact that a great many scientists are confused about this is no excuse. Genes include introns so the typical human gene is quite large. In fact, about 45% of the human genome is devoted to genes. This is a far cry from the small percentage (<2%) that consists only of coding regions.
  • Kat Arney says, "So, given that most of our genome isn’t actually genes, what does the rest of it do? Well, it’s complicated, and there’s still a lot we don’t know." My quibble here is subtle but I think it's important. I think we have a pretty good handle on the functional parts of our genome and I don't expect any surprises. We know that about 10% of our genome is conserved and we can account for most of that functional DNA. The rest is not a mystery. We know that most of it consists of various flotsam and jetsam related to transposons and things like pseudogenes and dead viruses. This is junk DNA by any definition and we should stop pretending that it's a big mystery. When we say that 90% of our genome is junk that's not a reflection of ignorance; it's an evidence-based conclusion.

Hatje, K., Mühlhausen, S., Simm, D., and Kollmar, M. (2019) The Protein-Coding Human Genome: Annotating High-Hanging Fruits. BioEssays, 0(0), 1900066. [doi: 10.1002/bies.201900066]

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